Starting phenix.real_space_refine on Fri Jul 3 19:22:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx2_44991/07_2026/9bx2_44991.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15954 At special positions: 0 Unit cell: (95.046, 140.014, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 663.4 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.273A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A 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: 3.565A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4844 1.33 - 1.46: 2960 1.46 - 1.58: 8319 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21460 2.10 - 4.21: 471 4.21 - 6.31: 58 6.31 - 8.42: 8 8.42 - 10.52: 7 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -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 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.71 10.52 3.00e+00 1.11e-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 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8646 17.66 - 35.32: 852 35.32 - 52.98: 254 52.98 - 70.64: 64 70.64 - 88.30: 40 Dihedral angle restraints: 9856 sinusoidal: 4110 harmonic: 5746 Sorted by residual: dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.38 12.38 0 2.50e+00 1.60e-01 2.45e+01 dihedral pdb=" N VAL C 125 " pdb=" C VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual 123.40 135.59 -12.19 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" C ASN C 98 " pdb=" N ASN C 98 " pdb=" CA ASN C 98 " pdb=" CB ASN C 98 " ideal model delta harmonic sigma weight residual -122.60 -134.32 11.72 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2126 0.094 - 0.187: 182 0.187 - 0.281: 33 0.281 - 0.374: 5 0.374 - 0.468: 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 5.47e+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 4.66e+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 2.92e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-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 1.10e-02 2.11e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11872 3.11 - 3.70: 26434 3.70 - 4.30: 41217 4.30 - 4.90: 64993 Nonbonded interactions: 144648 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 ... (remaining 144643 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: 0.010 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.070 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.834 16299 Z= 0.733 Angle : 0.756 10.524 22004 Z= 0.462 Chirality : 0.059 0.468 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.904 88.298 6168 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (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 ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.33 (16298) covalent geometry : angle 0.75633 / 0.46 (22004) hydrogen bonds : bond 0.16169 / 10.53 ( 896) hydrogen bonds : angle 6.35147 / 4.47 ( 2616) Misc. bond : bond 0.83443 / 43.92 ( 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 910 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 886 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 37 PHE cc_start: 0.7919 (m-80) cc_final: 0.7670 (m-80) REVERT: A 101 TYR cc_start: 0.8052 (m-80) cc_final: 0.7846 (m-80) REVERT: A 147 GLN cc_start: 0.8560 (mt0) cc_final: 0.7467 (mt0) REVERT: A 152 SER cc_start: 0.8560 (p) cc_final: 0.8218 (p) REVERT: A 179 LEU cc_start: 0.9405 (tp) cc_final: 0.9188 (tp) REVERT: A 181 ASP cc_start: 0.8156 (m-30) cc_final: 0.7915 (m-30) REVERT: A 188 ILE cc_start: 0.9049 (mt) cc_final: 0.8829 (mt) REVERT: A 232 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7971 (m-40) REVERT: A 246 SER cc_start: 0.8278 (m) cc_final: 0.8039 (p) REVERT: A 406 ASP cc_start: 0.7400 (m-30) cc_final: 0.7190 (m-30) REVERT: A 411 LEU cc_start: 0.8475 (mt) cc_final: 0.8056 (mp) REVERT: A 442 THR cc_start: 0.8764 (p) cc_final: 0.8349 (m) REVERT: A 583 SER cc_start: 0.8154 (m) cc_final: 0.7926 (t) REVERT: B 104 TYR cc_start: 0.7704 (m-80) cc_final: 0.7393 (m-80) REVERT: B 116 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 172 LEU cc_start: 0.9028 (mp) cc_final: 0.8479 (mp) REVERT: B 181 ASP cc_start: 0.8382 (m-30) cc_final: 0.7907 (m-30) REVERT: B 227 MET cc_start: 0.7932 (mtp) cc_final: 0.7487 (mtp) REVERT: B 267 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7823 (pt) REVERT: B 276 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8225 (mtmm) REVERT: B 280 ILE cc_start: 0.9081 (pt) cc_final: 0.8833 (pt) REVERT: B 294 GLU cc_start: 0.6773 (mt-10) cc_final: 0.4936 (mt-10) REVERT: B 358 ILE cc_start: 0.9388 (mm) cc_final: 0.9164 (mm) REVERT: B 375 LYS cc_start: 0.9185 (mptp) cc_final: 0.8940 (mmtp) REVERT: B 396 ASP cc_start: 0.7618 (m-30) cc_final: 0.7396 (m-30) REVERT: B 550 MET cc_start: 0.8110 (ttm) cc_final: 0.7665 (mtp) REVERT: B 583 SER cc_start: 0.8125 (m) cc_final: 0.7778 (t) REVERT: B 597 ILE cc_start: 0.9145 (pt) cc_final: 0.8926 (pt) REVERT: B 637 VAL cc_start: 0.9061 (t) cc_final: 0.8850 (t) REVERT: C 26 VAL cc_start: 0.7638 (m) cc_final: 0.7122 (m) REVERT: C 106 SER cc_start: 0.7849 (m) cc_final: 0.7089 (t) REVERT: C 153 LEU cc_start: 0.6349 (tp) cc_final: 0.5530 (tp) REVERT: C 229 ILE cc_start: 0.3543 (mt) cc_final: 0.3299 (mt) REVERT: C 316 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7776 (mtmm) REVERT: D 55 TYR cc_start: 0.5619 (t80) cc_final: 0.5408 (t80) REVERT: D 96 MET cc_start: 0.5853 (mmm) cc_final: 0.5391 (mmm) REVERT: D 178 PHE cc_start: 0.6543 (m-80) cc_final: 0.5485 (m-10) REVERT: D 256 VAL cc_start: 0.6468 (t) cc_final: 0.6261 (p) outliers start: 24 outliers final: 4 residues processed: 894 average time/residue: 0.1386 time to fit residues: 181.9687 Evaluate side-chains 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 540 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 14 ASN A 49 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 14 ASN B 232 ASN B 312 GLN B 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 25 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 101 HIS C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 283 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090178 restraints weight = 32206.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.093405 restraints weight = 15132.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095551 restraints weight = 9050.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096907 restraints weight = 6318.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097782 restraints weight = 4952.077| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16299 Z= 0.253 Angle : 0.704 10.353 22004 Z= 0.375 Chirality : 0.046 0.191 2348 Planarity : 0.004 0.053 2812 Dihedral : 7.201 63.755 2280 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.38 % Allowed : 17.39 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.19), residues: 1928 helix: 1.48 (0.15), residues: 1132 sheet: 0.37 (0.40), residues: 134 loop : 0.72 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 261 TYR 0.036 0.002 TYR D 262 PHE 0.023 0.002 PHE C 122 TRP 0.026 0.003 TRP C 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (16298) covalent geometry : angle 0.70359 / 0.38 (22004) hydrogen bonds : bond 0.04985 / 3.16 ( 896) hydrogen bonds : angle 5.23496 / 3.65 ( 2616) Misc. bond : bond 0.00119 / 0.06 ( 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 636 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 561 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7744 (mp0) REVERT: A 143 LEU cc_start: 0.9401 (tp) cc_final: 0.9144 (tp) REVERT: A 147 GLN cc_start: 0.9456 (mt0) cc_final: 0.9231 (mt0) REVERT: A 157 LEU cc_start: 0.9162 (tt) cc_final: 0.8718 (tp) REVERT: A 161 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7665 (mtm-85) REVERT: A 174 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 181 ASP cc_start: 0.8756 (m-30) cc_final: 0.8499 (m-30) REVERT: A 214 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8361 (mmtm) REVERT: A 246 SER cc_start: 0.7466 (m) cc_final: 0.7182 (p) REVERT: A 256 ARG cc_start: 0.8914 (tpt90) cc_final: 0.8653 (tpt90) REVERT: A 348 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8533 (tmm) REVERT: A 393 SER cc_start: 0.8757 (m) cc_final: 0.8471 (p) REVERT: A 509 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 583 SER cc_start: 0.8779 (m) cc_final: 0.8324 (t) REVERT: A 598 MET cc_start: 0.8061 (mtp) cc_final: 0.7507 (mtp) REVERT: A 599 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: A 640 MET cc_start: 0.8949 (tpp) cc_final: 0.8618 (tpp) REVERT: A 658 LEU cc_start: 0.9572 (mp) cc_final: 0.9307 (mt) REVERT: A 686 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7468 (mtp85) REVERT: B 54 LYS cc_start: 0.9484 (tttp) cc_final: 0.9262 (tptt) REVERT: B 64 TYR cc_start: 0.8666 (m-10) cc_final: 0.8439 (m-10) REVERT: B 102 ASN cc_start: 0.9302 (m-40) cc_final: 0.8848 (m110) REVERT: B 109 ASN cc_start: 0.9346 (OUTLIER) cc_final: 0.9033 (m110) REVERT: B 172 LEU cc_start: 0.8869 (mp) cc_final: 0.8653 (mp) REVERT: B 184 ARG cc_start: 0.9122 (tpp-160) cc_final: 0.8864 (tpp80) REVERT: B 317 MET cc_start: 0.8606 (mtm) cc_final: 0.8292 (mtt) REVERT: B 318 ASP cc_start: 0.8522 (t0) cc_final: 0.8267 (p0) REVERT: B 334 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8868 (ptpt) REVERT: B 466 MET cc_start: 0.8961 (ptt) cc_final: 0.8398 (ptp) REVERT: B 515 ASP cc_start: 0.9077 (m-30) cc_final: 0.8856 (m-30) REVERT: B 550 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: B 583 SER cc_start: 0.8932 (m) cc_final: 0.8670 (t) REVERT: B 599 GLU cc_start: 0.8715 (pt0) cc_final: 0.8500 (pm20) REVERT: B 602 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: B 604 ARG cc_start: 0.9056 (mmm160) cc_final: 0.8733 (mmm160) REVERT: C 20 MET cc_start: 0.9333 (mpp) cc_final: 0.8549 (tmm) REVERT: C 26 VAL cc_start: 0.9442 (m) cc_final: 0.9088 (m) REVERT: C 29 PHE cc_start: 0.6997 (p90) cc_final: 0.6715 (p90) REVERT: C 89 VAL cc_start: 0.8257 (t) cc_final: 0.7313 (t) REVERT: C 90 LEU cc_start: 0.9347 (mt) cc_final: 0.8907 (mt) REVERT: C 92 PHE cc_start: 0.9081 (t80) cc_final: 0.8782 (t80) REVERT: C 93 MET cc_start: 0.8300 (mtt) cc_final: 0.8017 (mtt) REVERT: C 96 MET cc_start: 0.8128 (mmm) cc_final: 0.7710 (mmm) REVERT: C 118 ILE cc_start: 0.8527 (mt) cc_final: 0.7963 (pt) REVERT: C 124 TRP cc_start: 0.7647 (t60) cc_final: 0.7137 (t60) REVERT: C 162 TYR cc_start: 0.8795 (m-10) cc_final: 0.8306 (m-80) REVERT: C 212 ILE cc_start: 0.7224 (mm) cc_final: 0.6702 (mm) REVERT: C 229 ILE cc_start: 0.5226 (mt) cc_final: 0.5016 (mt) REVERT: D 20 MET cc_start: 0.9364 (mmm) cc_final: 0.8888 (ptm) REVERT: D 21 PHE cc_start: 0.8363 (m-80) cc_final: 0.8042 (m-10) REVERT: D 25 ASN cc_start: 0.9515 (m-40) cc_final: 0.9256 (m-40) REVERT: D 30 TRP cc_start: 0.8067 (p-90) cc_final: 0.7286 (p-90) REVERT: D 93 MET cc_start: 0.6733 (ptm) cc_final: 0.6468 (ptm) REVERT: D 96 MET cc_start: 0.7473 (mmm) cc_final: 0.6992 (mmm) REVERT: D 162 TYR cc_start: 0.9001 (m-10) cc_final: 0.8601 (m-80) REVERT: D 178 PHE cc_start: 0.8755 (m-10) cc_final: 0.7998 (m-10) REVERT: D 213 TYR cc_start: 0.6963 (t80) cc_final: 0.6761 (t80) REVERT: D 224 LEU cc_start: 0.8245 (mt) cc_final: 0.7950 (mt) REVERT: D 227 PHE cc_start: 0.7871 (m-10) cc_final: 0.7606 (m-80) REVERT: D 259 PHE cc_start: 0.8395 (t80) cc_final: 0.8164 (t80) REVERT: D 320 PHE cc_start: 0.8664 (m-80) cc_final: 0.8368 (m-80) outliers start: 75 outliers final: 39 residues processed: 607 average time/residue: 0.1141 time to fit residues: 103.7515 Evaluate side-chains 539 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 494 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 645 GLN C 127 GLN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.088863 restraints weight = 32576.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.091979 restraints weight = 15219.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094048 restraints weight = 9327.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.095412 restraints weight = 6582.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.096337 restraints weight = 5190.354| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16299 Z= 0.217 Angle : 0.660 9.369 22004 Z= 0.346 Chirality : 0.044 0.178 2348 Planarity : 0.004 0.050 2812 Dihedral : 7.132 61.297 2268 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.62 % Allowed : 19.66 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1928 helix: 1.32 (0.15), residues: 1131 sheet: 0.12 (0.41), residues: 134 loop : 0.74 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.040 0.002 TYR D 142 PHE 0.029 0.002 PHE C 122 TRP 0.020 0.003 TRP C 44 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (16298) covalent geometry : angle 0.66005 / 0.35 (22004) hydrogen bonds : bond 0.04551 / 2.89 ( 896) hydrogen bonds : angle 5.10070 / 3.57 ( 2616) Misc. bond : bond 0.00200 / 0.11 ( 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 608 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 546 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8359 (mm-30) REVERT: A 143 LEU cc_start: 0.9398 (tp) cc_final: 0.9132 (tp) REVERT: A 157 LEU cc_start: 0.9204 (tt) cc_final: 0.8899 (tp) REVERT: A 164 ARG cc_start: 0.8213 (ptt90) cc_final: 0.7633 (ptt90) REVERT: A 174 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 181 ASP cc_start: 0.8758 (m-30) cc_final: 0.8522 (m-30) REVERT: A 214 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8407 (mmtm) REVERT: A 218 ASN cc_start: 0.9218 (t0) cc_final: 0.8937 (t0) REVERT: A 286 ASP cc_start: 0.8114 (m-30) cc_final: 0.7718 (m-30) REVERT: A 318 ASP cc_start: 0.8465 (t0) cc_final: 0.7575 (t0) REVERT: A 322 MET cc_start: 0.9280 (mmm) cc_final: 0.9078 (mmm) REVERT: A 334 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8415 (ptpt) REVERT: A 348 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8527 (tmm) REVERT: A 362 ASP cc_start: 0.8371 (m-30) cc_final: 0.7659 (m-30) REVERT: A 383 SER cc_start: 0.8943 (m) cc_final: 0.8572 (t) REVERT: A 393 SER cc_start: 0.8858 (m) cc_final: 0.8587 (p) REVERT: A 446 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7768 (mmp80) REVERT: A 509 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 598 MET cc_start: 0.8143 (mtp) cc_final: 0.6790 (mtp) REVERT: A 599 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: A 658 LEU cc_start: 0.9537 (mp) cc_final: 0.9303 (mt) REVERT: B 102 ASN cc_start: 0.9293 (m-40) cc_final: 0.8869 (m110) REVERT: B 104 TYR cc_start: 0.8965 (m-80) cc_final: 0.8539 (m-80) REVERT: B 109 ASN cc_start: 0.9428 (OUTLIER) cc_final: 0.8994 (m-40) REVERT: B 121 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.9172 (tpt170) REVERT: B 172 LEU cc_start: 0.8949 (mp) cc_final: 0.8410 (mp) REVERT: B 184 ARG cc_start: 0.9142 (tpp-160) cc_final: 0.8843 (tpp80) REVERT: B 238 ASP cc_start: 0.7921 (t0) cc_final: 0.7244 (t70) REVERT: B 274 ARG cc_start: 0.6625 (ttp-110) cc_final: 0.6059 (ttp-110) REVERT: B 322 MET cc_start: 0.9118 (mmm) cc_final: 0.8906 (mmm) REVERT: B 334 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8769 (ptpt) REVERT: B 381 LEU cc_start: 0.9369 (tt) cc_final: 0.9133 (tp) REVERT: B 415 ASN cc_start: 0.9151 (t0) cc_final: 0.8837 (t0) REVERT: B 418 ASN cc_start: 0.8840 (m110) cc_final: 0.8635 (m-40) REVERT: B 474 GLN cc_start: 0.8735 (mt0) cc_final: 0.8418 (mt0) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8836 (m-30) REVERT: B 550 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: B 570 MET cc_start: 0.8507 (mtp) cc_final: 0.8272 (mtp) REVERT: B 599 GLU cc_start: 0.8731 (pt0) cc_final: 0.8004 (pm20) REVERT: B 602 GLU cc_start: 0.8633 (tt0) cc_final: 0.7711 (tp30) REVERT: B 604 ARG cc_start: 0.9036 (mmm160) cc_final: 0.8441 (mmm160) REVERT: B 610 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8034 (mmmt) REVERT: B 639 ASP cc_start: 0.8427 (m-30) cc_final: 0.8112 (m-30) REVERT: C 20 MET cc_start: 0.9550 (mpp) cc_final: 0.9268 (ppp) REVERT: C 26 VAL cc_start: 0.9370 (m) cc_final: 0.9053 (m) REVERT: C 29 PHE cc_start: 0.6883 (p90) cc_final: 0.6661 (p90) REVERT: C 89 VAL cc_start: 0.8246 (t) cc_final: 0.7620 (t) REVERT: C 90 LEU cc_start: 0.9467 (mt) cc_final: 0.9106 (mt) REVERT: C 92 PHE cc_start: 0.9178 (t80) cc_final: 0.8712 (t80) REVERT: C 93 MET cc_start: 0.8790 (mtt) cc_final: 0.8132 (mtt) REVERT: C 95 MET cc_start: 0.8777 (tmm) cc_final: 0.8356 (tmm) REVERT: C 96 MET cc_start: 0.8310 (mmm) cc_final: 0.7569 (mmm) REVERT: C 109 PHE cc_start: 0.8314 (m-10) cc_final: 0.8086 (m-80) REVERT: C 118 ILE cc_start: 0.8321 (mt) cc_final: 0.8118 (pt) REVERT: C 124 TRP cc_start: 0.7825 (t60) cc_final: 0.7090 (t60) REVERT: C 129 LYS cc_start: 0.9436 (mmmt) cc_final: 0.8971 (mmmt) REVERT: C 162 TYR cc_start: 0.8833 (m-10) cc_final: 0.8318 (m-80) REVERT: C 178 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: D 21 PHE cc_start: 0.8366 (m-80) cc_final: 0.8067 (m-10) REVERT: D 25 ASN cc_start: 0.9617 (m-40) cc_final: 0.9374 (m-40) REVERT: D 56 MET cc_start: 0.8567 (ptt) cc_final: 0.8321 (mmp) REVERT: D 96 MET cc_start: 0.7351 (mmm) cc_final: 0.7056 (mmm) REVERT: D 134 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7108 (pttt) REVERT: D 148 ASP cc_start: 0.7624 (m-30) cc_final: 0.7424 (m-30) REVERT: D 174 TYR cc_start: 0.8656 (t80) cc_final: 0.8411 (t80) REVERT: D 178 PHE cc_start: 0.8780 (m-10) cc_final: 0.8431 (m-10) REVERT: D 213 TYR cc_start: 0.6947 (t80) cc_final: 0.6453 (t80) REVERT: D 227 PHE cc_start: 0.7872 (m-10) cc_final: 0.7601 (m-80) outliers start: 62 outliers final: 41 residues processed: 578 average time/residue: 0.1199 time to fit residues: 102.7871 Evaluate side-chains 566 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 516 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL 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 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.086638 restraints weight = 33013.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089734 restraints weight = 15727.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091772 restraints weight = 9408.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093092 restraints weight = 6623.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093967 restraints weight = 5229.339| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16299 Z= 0.229 Angle : 0.648 9.734 22004 Z= 0.340 Chirality : 0.044 0.200 2348 Planarity : 0.004 0.048 2812 Dihedral : 6.979 60.975 2266 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.32 % Allowed : 19.66 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1928 helix: 1.29 (0.15), residues: 1127 sheet: -0.16 (0.41), residues: 142 loop : 0.62 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.038 0.002 TYR D 130 PHE 0.053 0.002 PHE C 122 TRP 0.024 0.003 TRP C 30 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (16298) covalent geometry : angle 0.64802 / 0.34 (22004) hydrogen bonds : bond 0.04385 / 2.79 ( 896) hydrogen bonds : angle 5.03090 / 3.53 ( 2616) Misc. bond : bond 0.00057 / 0.03 ( 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 601 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 527 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8624 (mp0) cc_final: 0.8369 (mp0) REVERT: A 139 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 164 ARG cc_start: 0.8227 (ptt90) cc_final: 0.7566 (ptt90) REVERT: A 174 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 191 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8317 (mm-40) REVERT: A 214 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8422 (mmtm) REVERT: A 286 ASP cc_start: 0.8118 (m-30) cc_final: 0.7772 (m-30) REVERT: A 321 GLU cc_start: 0.7731 (mp0) cc_final: 0.7321 (mp0) REVERT: A 322 MET cc_start: 0.9302 (mmm) cc_final: 0.8986 (mmm) REVERT: A 334 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8360 (ptpt) REVERT: A 348 MET cc_start: 0.8856 (ttp) cc_final: 0.8549 (tmm) REVERT: A 362 ASP cc_start: 0.8486 (m-30) cc_final: 0.7523 (m-30) REVERT: A 383 SER cc_start: 0.8906 (m) cc_final: 0.8685 (t) REVERT: A 393 SER cc_start: 0.8897 (m) cc_final: 0.8260 (p) REVERT: A 415 ASN cc_start: 0.9030 (t0) cc_final: 0.8754 (t0) REVERT: A 492 PHE cc_start: 0.9458 (m-80) cc_final: 0.9247 (m-80) REVERT: A 509 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8400 (tm-30) REVERT: A 598 MET cc_start: 0.8167 (mtp) cc_final: 0.7091 (mtp) REVERT: A 599 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: A 602 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7146 (tp30) REVERT: A 604 ARG cc_start: 0.8541 (mtp85) cc_final: 0.7971 (mmp80) REVERT: A 632 MET cc_start: 0.9176 (mtm) cc_final: 0.8929 (mtm) REVERT: A 686 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6564 (mtp85) REVERT: B 102 ASN cc_start: 0.9281 (m-40) cc_final: 0.8868 (m110) REVERT: B 104 TYR cc_start: 0.9011 (m-80) cc_final: 0.8644 (m-80) REVERT: B 121 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9211 (tpt170) REVERT: B 172 LEU cc_start: 0.8932 (mp) cc_final: 0.8687 (mp) REVERT: B 179 LEU cc_start: 0.9529 (tp) cc_final: 0.9099 (tt) REVERT: B 184 ARG cc_start: 0.9140 (tpp-160) cc_final: 0.8845 (tpp80) REVERT: B 238 ASP cc_start: 0.8002 (t0) cc_final: 0.7188 (t0) REVERT: B 274 ARG cc_start: 0.6631 (ttp-110) cc_final: 0.6018 (ttp-110) REVERT: B 317 MET cc_start: 0.8538 (mtm) cc_final: 0.8176 (mtt) REVERT: B 334 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8783 (ptpt) REVERT: B 515 ASP cc_start: 0.9092 (m-30) cc_final: 0.8845 (m-30) REVERT: B 550 MET cc_start: 0.8215 (ttm) cc_final: 0.7935 (mtp) REVERT: B 599 GLU cc_start: 0.8750 (pt0) cc_final: 0.8014 (pm20) REVERT: B 602 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: B 604 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8466 (mmm160) REVERT: B 639 ASP cc_start: 0.8424 (m-30) cc_final: 0.8059 (m-30) REVERT: C 26 VAL cc_start: 0.9360 (m) cc_final: 0.9033 (m) REVERT: C 74 MET cc_start: 0.6916 (mtt) cc_final: 0.6445 (mtt) REVERT: C 89 VAL cc_start: 0.8259 (t) cc_final: 0.7663 (t) REVERT: C 90 LEU cc_start: 0.9520 (mt) cc_final: 0.9186 (mt) REVERT: C 92 PHE cc_start: 0.9227 (t80) cc_final: 0.8697 (t80) REVERT: C 93 MET cc_start: 0.8712 (mtt) cc_final: 0.8284 (mtt) REVERT: C 95 MET cc_start: 0.8837 (tmm) cc_final: 0.8263 (tmm) REVERT: C 96 MET cc_start: 0.8380 (mmm) cc_final: 0.7583 (mmm) REVERT: C 109 PHE cc_start: 0.8323 (m-10) cc_final: 0.8033 (m-80) REVERT: C 129 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9240 (mmmt) REVERT: C 162 TYR cc_start: 0.8854 (m-10) cc_final: 0.8189 (m-10) REVERT: C 197 ASP cc_start: 0.8837 (t70) cc_final: 0.8565 (t70) REVERT: C 271 LEU cc_start: 0.8524 (mt) cc_final: 0.8252 (mt) REVERT: D 20 MET cc_start: 0.9433 (mmm) cc_final: 0.8993 (ptm) REVERT: D 25 ASN cc_start: 0.9569 (m-40) cc_final: 0.9332 (m-40) REVERT: D 109 PHE cc_start: 0.8267 (m-80) cc_final: 0.7906 (m-80) REVERT: D 123 GLU cc_start: 0.9233 (tp30) cc_final: 0.9025 (tp30) REVERT: D 134 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7390 (pttt) REVERT: D 148 ASP cc_start: 0.7763 (m-30) cc_final: 0.7504 (m-30) REVERT: D 154 PHE cc_start: 0.8248 (t80) cc_final: 0.8017 (t80) REVERT: D 162 TYR cc_start: 0.8708 (m-80) cc_final: 0.8446 (m-80) REVERT: D 174 TYR cc_start: 0.8805 (t80) cc_final: 0.8597 (t80) REVERT: D 178 PHE cc_start: 0.8807 (m-10) cc_final: 0.8464 (m-10) REVERT: D 213 TYR cc_start: 0.6852 (t80) cc_final: 0.6508 (t80) REVERT: D 227 PHE cc_start: 0.8100 (m-10) cc_final: 0.7728 (m-80) REVERT: D 239 GLU cc_start: 0.7242 (pp20) cc_final: 0.6991 (pp20) REVERT: D 240 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6722 (pp) REVERT: D 260 ILE cc_start: 0.8142 (pt) cc_final: 0.7900 (pt) outliers start: 74 outliers final: 46 residues processed: 566 average time/residue: 0.1194 time to fit residues: 101.0082 Evaluate side-chains 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 493 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.089321 restraints weight = 32602.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092525 restraints weight = 15209.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094555 restraints weight = 9005.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095820 restraints weight = 6339.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096722 restraints weight = 4987.319| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16299 Z= 0.177 Angle : 0.637 10.175 22004 Z= 0.330 Chirality : 0.043 0.187 2348 Planarity : 0.004 0.045 2812 Dihedral : 6.773 61.397 2265 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.08 % Allowed : 21.94 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 1928 helix: 1.26 (0.15), residues: 1135 sheet: 0.47 (0.46), residues: 112 loop : 0.43 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.038 0.002 TYR D 142 PHE 0.040 0.002 PHE D 168 TRP 0.029 0.002 TRP C 30 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (16298) covalent geometry : angle 0.63696 / 0.33 (22004) hydrogen bonds : bond 0.04129 / 2.63 ( 896) hydrogen bonds : angle 4.97473 / 3.50 ( 2616) Misc. bond : bond 0.00044 / 0.02 ( 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 592 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 522 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8607 (mp0) cc_final: 0.8392 (mp0) REVERT: A 139 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 174 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 181 ASP cc_start: 0.8807 (m-30) cc_final: 0.8558 (m-30) REVERT: A 191 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 214 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8313 (mmtm) REVERT: A 286 ASP cc_start: 0.8183 (m-30) cc_final: 0.7960 (m-30) REVERT: A 322 MET cc_start: 0.9315 (mmm) cc_final: 0.9022 (mmm) REVERT: A 334 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8377 (ptpt) REVERT: A 335 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 348 MET cc_start: 0.8862 (ttp) cc_final: 0.8563 (tmm) REVERT: A 362 ASP cc_start: 0.8491 (m-30) cc_final: 0.7552 (m-30) REVERT: A 383 SER cc_start: 0.8871 (m) cc_final: 0.8653 (t) REVERT: A 393 SER cc_start: 0.8906 (m) cc_final: 0.8402 (p) REVERT: A 415 ASN cc_start: 0.8946 (t0) cc_final: 0.8671 (t0) REVERT: A 446 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7046 (mmp-170) REVERT: A 509 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 598 MET cc_start: 0.8193 (mtp) cc_final: 0.7287 (mtp) REVERT: A 599 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: A 602 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: A 604 ARG cc_start: 0.8509 (mtp85) cc_final: 0.7934 (mmp80) REVERT: B 78 LYS cc_start: 0.9140 (pttp) cc_final: 0.8902 (mtmm) REVERT: B 102 ASN cc_start: 0.9286 (m-40) cc_final: 0.8866 (m110) REVERT: B 104 TYR cc_start: 0.8973 (m-80) cc_final: 0.8615 (m-80) REVERT: B 109 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9089 (m-40) REVERT: B 172 LEU cc_start: 0.8944 (mp) cc_final: 0.8695 (mp) REVERT: B 179 LEU cc_start: 0.9495 (tp) cc_final: 0.9134 (tt) REVERT: B 238 ASP cc_start: 0.7972 (t0) cc_final: 0.7166 (t0) REVERT: B 274 ARG cc_start: 0.6646 (ttp-110) cc_final: 0.6018 (ttp-110) REVERT: B 334 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8817 (ptpt) REVERT: B 515 ASP cc_start: 0.9093 (m-30) cc_final: 0.8825 (m-30) REVERT: B 550 MET cc_start: 0.8178 (ttm) cc_final: 0.7926 (mtp) REVERT: B 570 MET cc_start: 0.8447 (mtp) cc_final: 0.8134 (mtp) REVERT: B 599 GLU cc_start: 0.8698 (pt0) cc_final: 0.8378 (pm20) REVERT: B 604 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8695 (mmm160) REVERT: B 610 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8154 (mmmt) REVERT: B 639 ASP cc_start: 0.8518 (m-30) cc_final: 0.8122 (m-30) REVERT: C 16 ASP cc_start: 0.5676 (m-30) cc_final: 0.5460 (m-30) REVERT: C 43 THR cc_start: 0.0330 (OUTLIER) cc_final: -0.0537 (p) REVERT: C 89 VAL cc_start: 0.8299 (t) cc_final: 0.7730 (t) REVERT: C 90 LEU cc_start: 0.9536 (mt) cc_final: 0.9202 (mt) REVERT: C 92 PHE cc_start: 0.9265 (t80) cc_final: 0.8711 (t80) REVERT: C 93 MET cc_start: 0.8895 (mtt) cc_final: 0.8568 (mtt) REVERT: C 95 MET cc_start: 0.8860 (tmm) cc_final: 0.8179 (tmm) REVERT: C 96 MET cc_start: 0.8392 (mmm) cc_final: 0.7751 (mmm) REVERT: C 109 PHE cc_start: 0.8238 (m-10) cc_final: 0.8028 (m-80) REVERT: C 162 TYR cc_start: 0.8799 (m-10) cc_final: 0.8101 (m-10) REVERT: C 198 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.9104 (mm-30) REVERT: C 226 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8803 (pp20) REVERT: C 271 LEU cc_start: 0.8523 (mt) cc_final: 0.8318 (mt) REVERT: D 21 PHE cc_start: 0.8468 (m-10) cc_final: 0.8202 (m-10) REVERT: D 25 ASN cc_start: 0.9576 (m-40) cc_final: 0.9366 (m-40) REVERT: D 56 MET cc_start: 0.9171 (mmp) cc_final: 0.8554 (ptp) REVERT: D 109 PHE cc_start: 0.8320 (m-80) cc_final: 0.8088 (m-80) REVERT: D 148 ASP cc_start: 0.7815 (m-30) cc_final: 0.7523 (m-30) REVERT: D 178 PHE cc_start: 0.8769 (m-10) cc_final: 0.8316 (m-10) REVERT: D 195 LEU cc_start: 0.8746 (mm) cc_final: 0.8545 (mm) REVERT: D 227 PHE cc_start: 0.8065 (m-10) cc_final: 0.7658 (m-80) REVERT: D 240 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6655 (pp) REVERT: D 261 ARG cc_start: 0.7462 (ttm170) cc_final: 0.6569 (ptm160) outliers start: 70 outliers final: 44 residues processed: 561 average time/residue: 0.1167 time to fit residues: 98.8042 Evaluate side-chains 545 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 493 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 180 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090385 restraints weight = 32407.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093607 restraints weight = 15035.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095618 restraints weight = 8801.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097046 restraints weight = 6094.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097840 restraints weight = 4749.788| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 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 = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5584 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= 0.154 Angle : 0.633 9.864 22004 Z= 0.329 Chirality : 0.043 0.183 2348 Planarity : 0.003 0.049 2812 Dihedral : 6.686 61.475 2265 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.62 % Allowed : 23.40 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1928 helix: 1.16 (0.15), residues: 1144 sheet: 0.57 (0.47), residues: 108 loop : 0.37 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.042 0.002 TYR D 142 PHE 0.037 0.002 PHE D 172 TRP 0.033 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16298) covalent geometry : angle 0.63271 / 0.33 (22004) hydrogen bonds : bond 0.03984 / 2.54 ( 896) hydrogen bonds : angle 4.96821 / 3.50 ( 2616) Misc. bond : bond 0.00040 / 0.02 ( 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 586 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 524 time to evaluate : 0.627 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 117 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8234 (mmm160) REVERT: A 135 GLU cc_start: 0.8632 (mp0) cc_final: 0.8395 (mp0) REVERT: A 139 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 174 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 181 ASP cc_start: 0.8754 (m-30) cc_final: 0.8489 (m-30) REVERT: A 214 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8217 (mmtm) REVERT: A 256 ARG cc_start: 0.8933 (tpt90) cc_final: 0.8393 (tpt90) REVERT: A 286 ASP cc_start: 0.8118 (m-30) cc_final: 0.7878 (m-30) REVERT: A 317 MET cc_start: 0.8280 (mtt) cc_final: 0.7982 (mtt) REVERT: A 334 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8383 (ptpt) REVERT: A 348 MET cc_start: 0.8855 (ttp) cc_final: 0.8535 (tmm) REVERT: A 350 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8037 (mtp85) REVERT: A 362 ASP cc_start: 0.8447 (m-30) cc_final: 0.7481 (m-30) REVERT: A 393 SER cc_start: 0.8752 (m) cc_final: 0.8349 (p) REVERT: A 446 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7152 (mmp-170) REVERT: A 509 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 598 MET cc_start: 0.8229 (mtp) cc_final: 0.7972 (mtp) REVERT: A 599 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: A 602 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: A 604 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8145 (mmp80) REVERT: B 78 LYS cc_start: 0.9134 (pttp) cc_final: 0.8796 (pttm) REVERT: B 95 MET cc_start: 0.9197 (tpp) cc_final: 0.8931 (tpp) REVERT: B 102 ASN cc_start: 0.9268 (m-40) cc_final: 0.8895 (m110) REVERT: B 104 TYR cc_start: 0.8969 (m-80) cc_final: 0.8636 (m-80) REVERT: B 161 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7870 (mtt180) REVERT: B 167 LEU cc_start: 0.8593 (mt) cc_final: 0.8305 (mt) REVERT: B 172 LEU cc_start: 0.8977 (mp) cc_final: 0.8448 (mp) REVERT: B 181 ASP cc_start: 0.8700 (m-30) cc_final: 0.8282 (m-30) REVERT: B 184 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8853 (tpp80) REVERT: B 238 ASP cc_start: 0.7936 (t0) cc_final: 0.7200 (t70) REVERT: B 274 ARG cc_start: 0.6656 (ttp-110) cc_final: 0.6151 (ttp-110) REVERT: B 334 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8870 (ptpt) REVERT: B 515 ASP cc_start: 0.9072 (m-30) cc_final: 0.8794 (m-30) REVERT: B 570 MET cc_start: 0.8447 (mtp) cc_final: 0.8158 (mtp) REVERT: B 599 GLU cc_start: 0.8698 (pt0) cc_final: 0.8352 (pm20) REVERT: B 604 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8597 (mmm160) REVERT: B 610 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8220 (mmmt) REVERT: B 639 ASP cc_start: 0.8542 (m-30) cc_final: 0.8104 (m-30) REVERT: B 686 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7732 (mmt180) REVERT: C 29 PHE cc_start: 0.6928 (p90) cc_final: 0.6698 (p90) REVERT: C 74 MET cc_start: 0.7126 (mtt) cc_final: 0.6916 (mtt) REVERT: C 89 VAL cc_start: 0.8380 (t) cc_final: 0.7683 (t) REVERT: C 90 LEU cc_start: 0.9567 (mt) cc_final: 0.9288 (mt) REVERT: C 93 MET cc_start: 0.9030 (mtt) cc_final: 0.8612 (mtt) REVERT: C 109 PHE cc_start: 0.8262 (m-10) cc_final: 0.7463 (m-80) REVERT: C 122 PHE cc_start: 0.9249 (t80) cc_final: 0.9024 (t80) REVERT: C 162 TYR cc_start: 0.8760 (m-10) cc_final: 0.8152 (m-10) REVERT: C 226 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8735 (pp20) REVERT: C 237 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9094 (pp20) REVERT: D 20 MET cc_start: 0.9501 (mmm) cc_final: 0.9122 (ptm) REVERT: D 21 PHE cc_start: 0.8444 (m-10) cc_final: 0.8120 (m-80) REVERT: D 25 ASN cc_start: 0.9599 (m-40) cc_final: 0.9302 (m110) REVERT: D 56 MET cc_start: 0.9176 (mmp) cc_final: 0.8481 (ptp) REVERT: D 109 PHE cc_start: 0.8405 (m-80) cc_final: 0.8183 (m-80) REVERT: D 134 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7788 (pttt) REVERT: D 148 ASP cc_start: 0.7718 (m-30) cc_final: 0.7394 (m-30) REVERT: D 174 TYR cc_start: 0.8690 (t80) cc_final: 0.8407 (t80) REVERT: D 227 PHE cc_start: 0.8248 (m-10) cc_final: 0.7845 (m-80) REVERT: D 261 ARG cc_start: 0.7599 (ttm170) cc_final: 0.6513 (ptm160) outliers start: 62 outliers final: 42 residues processed: 554 average time/residue: 0.1169 time to fit residues: 97.2333 Evaluate side-chains 539 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 492 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 21 optimal weight: 0.0000 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 418 ASN B 646 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN C 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095543 restraints weight = 32405.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098814 restraints weight = 14760.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100927 restraints weight = 8634.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102178 restraints weight = 5958.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103099 restraints weight = 4668.452| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.131 Angle : 0.651 15.778 22004 Z= 0.335 Chirality : 0.044 0.220 2348 Planarity : 0.003 0.051 2812 Dihedral : 6.576 62.353 2264 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.86 % Allowed : 23.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1928 helix: 1.16 (0.15), residues: 1137 sheet: 0.23 (0.43), residues: 126 loop : 0.39 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 261 TYR 0.046 0.002 TYR A 571 PHE 0.027 0.001 PHE D 168 TRP 0.033 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16298) covalent geometry : angle 0.65123 / 0.33 (22004) hydrogen bonds : bond 0.03921 / 2.51 ( 896) hydrogen bonds : angle 4.96600 / 3.50 ( 2616) Misc. bond : bond 0.00034 / 0.02 ( 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 570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 521 time to evaluate : 0.605 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 11 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: A 115 LEU cc_start: 0.8985 (mp) cc_final: 0.8434 (mt) REVERT: A 119 GLU cc_start: 0.8474 (mp0) cc_final: 0.7964 (mp0) REVERT: A 135 GLU cc_start: 0.8614 (mp0) cc_final: 0.8411 (mp0) REVERT: A 139 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8407 (mm-30) REVERT: A 174 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 181 ASP cc_start: 0.8782 (m-30) cc_final: 0.8547 (m-30) REVERT: A 214 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8164 (mmtm) REVERT: A 286 ASP cc_start: 0.8038 (m-30) cc_final: 0.7835 (m-30) REVERT: A 317 MET cc_start: 0.8318 (mtt) cc_final: 0.8041 (mtt) REVERT: A 334 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8249 (ptpt) REVERT: A 348 MET cc_start: 0.8896 (ttp) cc_final: 0.8664 (tmm) REVERT: A 350 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8217 (mtp85) REVERT: A 362 ASP cc_start: 0.8398 (m-30) cc_final: 0.7466 (m-30) REVERT: A 393 SER cc_start: 0.8597 (m) cc_final: 0.8221 (p) REVERT: A 446 ARG cc_start: 0.7754 (mmp80) cc_final: 0.7315 (mmp80) REVERT: A 509 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 598 MET cc_start: 0.8209 (mtp) cc_final: 0.7971 (mtp) REVERT: A 599 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 602 GLU cc_start: 0.7966 (tt0) cc_final: 0.7458 (tp30) REVERT: A 604 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8274 (mmp80) REVERT: A 657 PHE cc_start: 0.9077 (m-80) cc_final: 0.8797 (m-80) REVERT: B 78 LYS cc_start: 0.9155 (pttp) cc_final: 0.8910 (pttp) REVERT: B 95 MET cc_start: 0.9123 (tpp) cc_final: 0.8654 (tpp) REVERT: B 102 ASN cc_start: 0.9238 (m-40) cc_final: 0.8903 (m110) REVERT: B 104 TYR cc_start: 0.8926 (m-80) cc_final: 0.8578 (m-80) REVERT: B 161 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7842 (mtt180) REVERT: B 172 LEU cc_start: 0.8823 (mp) cc_final: 0.8529 (mp) REVERT: B 181 ASP cc_start: 0.8645 (m-30) cc_final: 0.8234 (m-30) REVERT: B 184 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8879 (tpp80) REVERT: B 232 ASN cc_start: 0.8794 (m-40) cc_final: 0.8536 (m110) REVERT: B 235 ARG cc_start: 0.8776 (ttp-110) cc_final: 0.8092 (ttm110) REVERT: B 238 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7201 (t70) REVERT: B 274 ARG cc_start: 0.6946 (ttp-110) cc_final: 0.6411 (ttp-110) REVERT: B 318 ASP cc_start: 0.8411 (t0) cc_final: 0.8110 (p0) REVERT: B 334 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8889 (ptpt) REVERT: B 515 ASP cc_start: 0.9029 (m-30) cc_final: 0.8746 (m-30) REVERT: B 570 MET cc_start: 0.8466 (mtp) cc_final: 0.8210 (mtp) REVERT: B 586 TYR cc_start: 0.9028 (m-80) cc_final: 0.8517 (m-80) REVERT: B 599 GLU cc_start: 0.8685 (pt0) cc_final: 0.8349 (pm20) REVERT: B 639 ASP cc_start: 0.8566 (m-30) cc_final: 0.8105 (m-30) REVERT: B 686 ARG cc_start: 0.7988 (mmt180) cc_final: 0.7725 (mmt180) REVERT: C 74 MET cc_start: 0.7062 (mtt) cc_final: 0.6851 (mtt) REVERT: C 89 VAL cc_start: 0.8352 (t) cc_final: 0.7761 (t) REVERT: C 90 LEU cc_start: 0.9589 (mt) cc_final: 0.9325 (mt) REVERT: C 93 MET cc_start: 0.9082 (mtt) cc_final: 0.8744 (mtt) REVERT: C 105 TYR cc_start: 0.5839 (p90) cc_final: 0.5282 (p90) REVERT: C 122 PHE cc_start: 0.9158 (t80) cc_final: 0.8918 (t80) REVERT: C 124 TRP cc_start: 0.8115 (t60) cc_final: 0.7653 (t60) REVERT: C 178 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: C 226 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8722 (pp20) REVERT: C 237 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9146 (pp20) REVERT: D 20 MET cc_start: 0.9489 (mmm) cc_final: 0.9112 (ptm) REVERT: D 21 PHE cc_start: 0.8529 (m-10) cc_final: 0.8209 (m-80) REVERT: D 25 ASN cc_start: 0.9543 (m-40) cc_final: 0.9254 (m110) REVERT: D 56 MET cc_start: 0.9163 (mmp) cc_final: 0.8458 (ptp) REVERT: D 109 PHE cc_start: 0.8432 (m-80) cc_final: 0.8204 (m-80) REVERT: D 134 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7697 (pttt) REVERT: D 148 ASP cc_start: 0.7763 (m-30) cc_final: 0.7401 (m-30) REVERT: D 174 TYR cc_start: 0.8794 (t80) cc_final: 0.8502 (t80) REVERT: D 189 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7990 (tm-30) REVERT: D 213 TYR cc_start: 0.6766 (t80) cc_final: 0.6383 (t80) REVERT: D 227 PHE cc_start: 0.8359 (m-10) cc_final: 0.7977 (m-80) REVERT: D 261 ARG cc_start: 0.7342 (ttm170) cc_final: 0.6781 (ptm160) outliers start: 49 outliers final: 29 residues processed: 546 average time/residue: 0.1219 time to fit residues: 99.8616 Evaluate side-chains 514 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 478 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN C 181 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.089437 restraints weight = 32825.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092490 restraints weight = 15295.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094506 restraints weight = 9127.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095794 restraints weight = 6379.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096683 restraints weight = 5001.059| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16299 Z= 0.206 Angle : 0.694 13.768 22004 Z= 0.358 Chirality : 0.045 0.239 2348 Planarity : 0.004 0.047 2812 Dihedral : 6.734 64.209 2264 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.03 % Allowed : 25.03 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1928 helix: 1.07 (0.15), residues: 1137 sheet: 0.19 (0.44), residues: 126 loop : 0.24 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.038 0.002 TYR D 142 PHE 0.038 0.002 PHE C 109 TRP 0.036 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (16298) covalent geometry : angle 0.69359 / 0.36 (22004) hydrogen bonds : bond 0.03953 / 2.55 ( 896) hydrogen bonds : angle 5.04626 / 3.56 ( 2616) Misc. bond : bond 0.00033 / 0.02 ( 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 552 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 500 time to evaluate : 0.573 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 11 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: A 117 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8240 (mmm160) REVERT: A 119 GLU cc_start: 0.8466 (mp0) cc_final: 0.7952 (mp0) REVERT: A 166 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 174 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 181 ASP cc_start: 0.8753 (m-30) cc_final: 0.8525 (m-30) REVERT: A 214 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8269 (mmtm) REVERT: A 286 ASP cc_start: 0.8133 (m-30) cc_final: 0.7879 (m-30) REVERT: A 317 MET cc_start: 0.8457 (mtt) cc_final: 0.8206 (mtt) REVERT: A 334 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: A 348 MET cc_start: 0.8908 (ttp) cc_final: 0.8656 (tmm) REVERT: A 350 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8049 (mtp85) REVERT: A 362 ASP cc_start: 0.8467 (m-30) cc_final: 0.7447 (m-30) REVERT: A 393 SER cc_start: 0.8944 (m) cc_final: 0.8567 (p) REVERT: A 446 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7434 (mmp80) REVERT: A 453 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (ttt-90) REVERT: A 483 GLU cc_start: 0.8895 (mp0) cc_final: 0.8518 (pm20) REVERT: A 509 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 599 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: A 602 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: A 604 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8304 (mmp80) REVERT: A 637 VAL cc_start: 0.9425 (t) cc_final: 0.9135 (p) REVERT: A 686 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7360 (mtp85) REVERT: B 78 LYS cc_start: 0.9182 (pttp) cc_final: 0.8941 (pttp) REVERT: B 102 ASN cc_start: 0.9232 (m-40) cc_final: 0.8892 (m110) REVERT: B 104 TYR cc_start: 0.9119 (m-80) cc_final: 0.8687 (m-80) REVERT: B 161 ARG cc_start: 0.8250 (mtt180) cc_final: 0.8008 (mtt180) REVERT: B 181 ASP cc_start: 0.8750 (m-30) cc_final: 0.8296 (m-30) REVERT: B 184 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8901 (tpp80) REVERT: B 235 ARG cc_start: 0.8765 (ttp-110) cc_final: 0.8471 (mtm-85) REVERT: B 238 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7120 (t70) REVERT: B 274 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6441 (ttp-110) REVERT: B 322 MET cc_start: 0.9120 (mmm) cc_final: 0.8851 (mmm) REVERT: B 334 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8811 (ptpt) REVERT: B 463 LEU cc_start: 0.9310 (tp) cc_final: 0.8988 (tp) REVERT: B 515 ASP cc_start: 0.9085 (m-30) cc_final: 0.8785 (m-30) REVERT: B 570 MET cc_start: 0.8432 (mtp) cc_final: 0.8144 (mtp) REVERT: B 586 TYR cc_start: 0.9036 (m-80) cc_final: 0.8620 (m-80) REVERT: B 599 GLU cc_start: 0.8717 (pt0) cc_final: 0.8018 (pm20) REVERT: B 602 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: B 610 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8325 (mmmt) REVERT: B 639 ASP cc_start: 0.8524 (m-30) cc_final: 0.8075 (m-30) REVERT: C 17 PHE cc_start: 0.7559 (p90) cc_final: 0.6307 (p90) REVERT: C 74 MET cc_start: 0.7276 (mtt) cc_final: 0.7066 (mtt) REVERT: C 89 VAL cc_start: 0.8585 (t) cc_final: 0.7979 (t) REVERT: C 90 LEU cc_start: 0.9591 (mt) cc_final: 0.9375 (mt) REVERT: C 93 MET cc_start: 0.9083 (mtt) cc_final: 0.8718 (mtt) REVERT: C 122 PHE cc_start: 0.9170 (t80) cc_final: 0.8889 (t80) REVERT: C 158 VAL cc_start: 0.9532 (t) cc_final: 0.8815 (m) REVERT: C 162 TYR cc_start: 0.8789 (m-10) cc_final: 0.8301 (m-10) REVERT: C 226 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8688 (pp20) REVERT: D 20 MET cc_start: 0.9513 (mmm) cc_final: 0.9137 (ptm) REVERT: D 21 PHE cc_start: 0.8548 (m-10) cc_final: 0.8272 (m-80) REVERT: D 25 ASN cc_start: 0.9615 (m-40) cc_final: 0.9288 (m110) REVERT: D 51 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8372 (mm-30) REVERT: D 56 MET cc_start: 0.9188 (mmp) cc_final: 0.8487 (ptp) REVERT: D 109 PHE cc_start: 0.8584 (m-80) cc_final: 0.8260 (m-80) REVERT: D 134 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7361 (pttp) REVERT: D 148 ASP cc_start: 0.7757 (m-30) cc_final: 0.7401 (m-30) REVERT: D 174 TYR cc_start: 0.8944 (t80) cc_final: 0.8651 (t80) REVERT: D 227 PHE cc_start: 0.8413 (m-10) cc_final: 0.8003 (m-80) REVERT: D 239 GLU cc_start: 0.7048 (pp20) cc_final: 0.6717 (pp20) REVERT: D 261 ARG cc_start: 0.7264 (ttm170) cc_final: 0.6728 (ptm160) outliers start: 52 outliers final: 33 residues processed: 527 average time/residue: 0.1204 time to fit residues: 94.5254 Evaluate side-chains 523 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 481 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 191 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.0010 chunk 63 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094615 restraints weight = 32612.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097926 restraints weight = 14951.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100087 restraints weight = 8712.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101441 restraints weight = 6027.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102350 restraints weight = 4677.597| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16299 Z= 0.145 Angle : 0.707 13.876 22004 Z= 0.360 Chirality : 0.045 0.279 2348 Planarity : 0.003 0.047 2812 Dihedral : 6.631 64.997 2264 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.10 % Allowed : 26.14 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1928 helix: 1.05 (0.15), residues: 1136 sheet: 0.07 (0.44), residues: 128 loop : 0.31 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.055 0.002 TYR C 55 PHE 0.043 0.002 PHE C 109 TRP 0.029 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (16298) covalent geometry : angle 0.70698 / 0.36 (22004) hydrogen bonds : bond 0.03924 / 2.53 ( 896) hydrogen bonds : angle 5.07686 / 3.57 ( 2616) Misc. bond : bond 0.00038 / 0.02 ( 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 546 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 510 time to evaluate : 0.611 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 11 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: A 95 MET cc_start: 0.9052 (tpp) cc_final: 0.8832 (tpp) REVERT: A 115 LEU cc_start: 0.8988 (mp) cc_final: 0.8458 (mt) REVERT: A 117 ARG cc_start: 0.8594 (mmm160) cc_final: 0.8170 (mmm160) REVERT: A 119 GLU cc_start: 0.8455 (mp0) cc_final: 0.7943 (mp0) REVERT: A 166 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 174 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 214 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8180 (mmtm) REVERT: A 286 ASP cc_start: 0.8020 (m-30) cc_final: 0.7804 (m-30) REVERT: A 317 MET cc_start: 0.8466 (mtt) cc_final: 0.8162 (mtt) REVERT: A 334 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8226 (ptpt) REVERT: A 348 MET cc_start: 0.8888 (ttp) cc_final: 0.8647 (tmm) REVERT: A 350 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8184 (mtp85) REVERT: A 362 ASP cc_start: 0.8380 (m-30) cc_final: 0.7404 (m-30) REVERT: A 446 ARG cc_start: 0.7812 (mmp80) cc_final: 0.7351 (mmp80) REVERT: A 483 GLU cc_start: 0.8926 (mp0) cc_final: 0.8524 (pm20) REVERT: A 509 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 599 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: A 602 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: B 78 LYS cc_start: 0.9138 (pttp) cc_final: 0.8902 (pttp) REVERT: B 102 ASN cc_start: 0.9186 (m-40) cc_final: 0.8844 (m110) REVERT: B 104 TYR cc_start: 0.9053 (m-80) cc_final: 0.8658 (m-80) REVERT: B 147 GLN cc_start: 0.9257 (mm110) cc_final: 0.8995 (mm110) REVERT: B 161 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7951 (mtt180) REVERT: B 181 ASP cc_start: 0.8642 (m-30) cc_final: 0.8179 (m-30) REVERT: B 184 ARG cc_start: 0.9111 (tpp-160) cc_final: 0.8717 (tpp80) REVERT: B 232 ASN cc_start: 0.8810 (m-40) cc_final: 0.8459 (m110) REVERT: B 235 ARG cc_start: 0.8872 (ttp-110) cc_final: 0.8406 (ttm110) REVERT: B 238 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7176 (t70) REVERT: B 250 TYR cc_start: 0.9211 (m-80) cc_final: 0.8900 (m-80) REVERT: B 334 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8817 (ptpp) REVERT: B 463 LEU cc_start: 0.9162 (tp) cc_final: 0.8865 (tp) REVERT: B 515 ASP cc_start: 0.9037 (m-30) cc_final: 0.8799 (m-30) REVERT: B 570 MET cc_start: 0.8427 (mtp) cc_final: 0.8165 (mtp) REVERT: B 586 TYR cc_start: 0.8999 (m-80) cc_final: 0.8734 (m-80) REVERT: B 599 GLU cc_start: 0.8682 (pt0) cc_final: 0.7955 (pm20) REVERT: B 602 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: B 604 ARG cc_start: 0.8731 (mmm160) cc_final: 0.7968 (mmm160) REVERT: B 610 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8279 (mmmt) REVERT: B 639 ASP cc_start: 0.8579 (m-30) cc_final: 0.8084 (m-30) REVERT: B 686 ARG cc_start: 0.7945 (mmt180) cc_final: 0.7713 (mmt180) REVERT: C 74 MET cc_start: 0.7210 (mtt) cc_final: 0.6986 (mtt) REVERT: C 89 VAL cc_start: 0.8646 (t) cc_final: 0.8067 (t) REVERT: C 93 MET cc_start: 0.9056 (mtt) cc_final: 0.8768 (mtt) REVERT: C 122 PHE cc_start: 0.9106 (t80) cc_final: 0.8803 (t80) REVERT: C 158 VAL cc_start: 0.9552 (t) cc_final: 0.8839 (m) REVERT: C 162 TYR cc_start: 0.8800 (m-10) cc_final: 0.8313 (m-10) REVERT: C 226 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8707 (pp20) REVERT: D 20 MET cc_start: 0.9487 (mmm) cc_final: 0.9153 (ptm) REVERT: D 21 PHE cc_start: 0.8591 (m-10) cc_final: 0.8345 (m-10) REVERT: D 25 ASN cc_start: 0.9570 (m-40) cc_final: 0.9270 (m110) REVERT: D 56 MET cc_start: 0.9173 (mmp) cc_final: 0.8470 (ptp) REVERT: D 79 GLU cc_start: 0.8372 (tm-30) cc_final: 0.6918 (mm-30) REVERT: D 109 PHE cc_start: 0.8485 (m-80) cc_final: 0.8183 (m-80) REVERT: D 134 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8005 (pttm) REVERT: D 148 ASP cc_start: 0.7874 (m-30) cc_final: 0.7532 (m-30) REVERT: D 157 MET cc_start: 0.6711 (ppp) cc_final: 0.6500 (ppp) REVERT: D 174 TYR cc_start: 0.8941 (t80) cc_final: 0.8624 (t80) REVERT: D 189 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8067 (tm-30) REVERT: D 227 PHE cc_start: 0.8495 (m-10) cc_final: 0.8174 (m-80) REVERT: D 261 ARG cc_start: 0.7524 (ttm170) cc_final: 0.6981 (ptm160) outliers start: 36 outliers final: 26 residues processed: 528 average time/residue: 0.1159 time to fit residues: 92.2661 Evaluate side-chains 519 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 485 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.093366 restraints weight = 32619.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096594 restraints weight = 15154.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098721 restraints weight = 8866.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100073 restraints weight = 6156.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101014 restraints weight = 4797.214| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16299 Z= 0.148 Angle : 0.714 12.412 22004 Z= 0.365 Chirality : 0.045 0.285 2348 Planarity : 0.003 0.046 2812 Dihedral : 6.527 66.323 2264 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.16 % Allowed : 26.78 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1928 helix: 0.96 (0.15), residues: 1151 sheet: -0.03 (0.44), residues: 128 loop : 0.04 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.050 0.002 TYR C 55 PHE 0.040 0.002 PHE C 109 TRP 0.032 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16298) covalent geometry : angle 0.71447 / 0.36 (22004) hydrogen bonds : bond 0.03930 / 2.55 ( 896) hydrogen bonds : angle 5.09244 / 3.59 ( 2616) Misc. bond : bond 0.00035 / 0.02 ( 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 530 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 493 time to evaluate : 0.568 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 11 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (mt0) REVERT: A 95 MET cc_start: 0.9081 (tpp) cc_final: 0.8867 (tpp) REVERT: A 115 LEU cc_start: 0.9003 (mp) cc_final: 0.8480 (mt) REVERT: A 117 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8154 (mmm160) REVERT: A 119 GLU cc_start: 0.8422 (mp0) cc_final: 0.7917 (mp0) REVERT: A 150 GLN cc_start: 0.8628 (tt0) cc_final: 0.8349 (tt0) REVERT: A 174 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 214 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8132 (mmtm) REVERT: A 286 ASP cc_start: 0.8008 (m-30) cc_final: 0.7799 (m-30) REVERT: A 317 MET cc_start: 0.8470 (mtt) cc_final: 0.8167 (mtt) REVERT: A 348 MET cc_start: 0.8886 (ttp) cc_final: 0.8653 (tmm) REVERT: A 350 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8202 (mtp85) REVERT: A 362 ASP cc_start: 0.8376 (m-30) cc_final: 0.7380 (m-30) REVERT: A 393 SER cc_start: 0.8527 (p) cc_final: 0.7470 (t) REVERT: A 446 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7329 (mmp80) REVERT: A 453 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8934 (ttt-90) REVERT: A 483 GLU cc_start: 0.8927 (mp0) cc_final: 0.8519 (pm20) REVERT: A 509 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 599 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: B 78 LYS cc_start: 0.9128 (pttp) cc_final: 0.8893 (pttp) REVERT: B 102 ASN cc_start: 0.9181 (m-40) cc_final: 0.8866 (m110) REVERT: B 104 TYR cc_start: 0.9029 (m-80) cc_final: 0.8666 (m-80) REVERT: B 147 GLN cc_start: 0.9256 (mm110) cc_final: 0.9034 (mm110) REVERT: B 161 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7960 (mtt180) REVERT: B 181 ASP cc_start: 0.8635 (m-30) cc_final: 0.8268 (m-30) REVERT: B 184 ARG cc_start: 0.9114 (tpp-160) cc_final: 0.8897 (tpp80) REVERT: B 235 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8539 (mtm-85) REVERT: B 238 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7177 (t70) REVERT: B 250 TYR cc_start: 0.9203 (m-80) cc_final: 0.8917 (m-80) REVERT: B 318 ASP cc_start: 0.8432 (t0) cc_final: 0.8077 (p0) REVERT: B 334 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8881 (ptpp) REVERT: B 427 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8685 (ptpp) REVERT: B 463 LEU cc_start: 0.9180 (tp) cc_final: 0.8890 (tp) REVERT: B 515 ASP cc_start: 0.9053 (m-30) cc_final: 0.8796 (m-30) REVERT: B 570 MET cc_start: 0.8444 (mtp) cc_final: 0.8175 (mtp) REVERT: B 599 GLU cc_start: 0.8681 (pt0) cc_final: 0.7940 (pm20) REVERT: B 602 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: B 604 ARG cc_start: 0.8693 (mmm160) cc_final: 0.7981 (mmm160) REVERT: B 610 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8348 (mmmt) REVERT: B 639 ASP cc_start: 0.8616 (m-30) cc_final: 0.8115 (m-30) REVERT: B 686 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7604 (mmt180) REVERT: C 74 MET cc_start: 0.7217 (mtt) cc_final: 0.6509 (mtm) REVERT: C 89 VAL cc_start: 0.8705 (t) cc_final: 0.8241 (t) REVERT: C 93 MET cc_start: 0.9006 (mtt) cc_final: 0.8727 (mtt) REVERT: C 122 PHE cc_start: 0.9056 (t80) cc_final: 0.8740 (t80) REVERT: C 158 VAL cc_start: 0.9539 (t) cc_final: 0.8826 (m) REVERT: C 162 TYR cc_start: 0.8831 (m-10) cc_final: 0.8394 (m-10) REVERT: C 226 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8726 (pp20) REVERT: D 20 MET cc_start: 0.9503 (mmm) cc_final: 0.9151 (ptm) REVERT: D 21 PHE cc_start: 0.8649 (m-10) cc_final: 0.8424 (m-10) REVERT: D 25 ASN cc_start: 0.9564 (m-40) cc_final: 0.9236 (m110) REVERT: D 56 MET cc_start: 0.9185 (mmp) cc_final: 0.8464 (ptp) REVERT: D 79 GLU cc_start: 0.8358 (tm-30) cc_final: 0.6945 (mm-30) REVERT: D 109 PHE cc_start: 0.8535 (m-80) cc_final: 0.8192 (m-80) REVERT: D 134 LYS cc_start: 0.8261 (pttt) cc_final: 0.7963 (pttm) REVERT: D 148 ASP cc_start: 0.7899 (m-30) cc_final: 0.7567 (m-30) REVERT: D 157 MET cc_start: 0.6766 (ppp) cc_final: 0.6498 (ppp) REVERT: D 174 TYR cc_start: 0.9030 (t80) cc_final: 0.8644 (t80) REVERT: D 227 PHE cc_start: 0.8532 (m-10) cc_final: 0.8194 (m-80) REVERT: D 261 ARG cc_start: 0.7442 (ttm170) cc_final: 0.6898 (ptm160) outliers start: 37 outliers final: 29 residues processed: 513 average time/residue: 0.1180 time to fit residues: 91.1373 Evaluate side-chains 511 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 476 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 162 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.134382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094345 restraints weight = 32467.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097669 restraints weight = 15088.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.099772 restraints weight = 8815.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101152 restraints weight = 6125.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101987 restraints weight = 4747.450| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16299 Z= 0.145 Angle : 0.729 13.082 22004 Z= 0.371 Chirality : 0.046 0.276 2348 Planarity : 0.003 0.043 2812 Dihedral : 6.416 65.539 2264 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 27.65 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1928 helix: 0.97 (0.15), residues: 1142 sheet: 0.02 (0.44), residues: 126 loop : 0.09 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.044 0.002 TYR C 55 PHE 0.038 0.002 PHE C 109 TRP 0.033 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16298) covalent geometry : angle 0.72945 / 0.37 (22004) hydrogen bonds : bond 0.03934 / 2.54 ( 896) hydrogen bonds : angle 5.10842 / 3.59 ( 2616) Misc. bond : bond 0.00035 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.85 seconds wall clock time: 56 minutes 7.02 seconds (3367.02 seconds total)