Starting phenix.real_space_refine on Sun Aug 24 00:49:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwx_44985/08_2025/9bwx_44985.map" } resolution = 2.91 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.79, per 1000 atoms: 0.24 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 134.904, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 394.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A 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: 3.638A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.547A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A 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: 5.842A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.173A 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: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A 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: 6.313A 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: 4.314A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.889A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.057A 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: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4956 1.34 - 1.46: 2920 1.46 - 1.58: 8247 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.76e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.18e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21496 2.09 - 4.17: 471 4.17 - 6.26: 33 6.26 - 8.35: 2 8.35 - 10.43: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.62 -6.08 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 SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9429 34.31 - 68.63: 329 68.63 - 102.94: 48 102.94 - 137.25: 0 137.25 - 171.56: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.12 171.56 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.69 165.99 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2126 0.093 - 0.187: 183 0.187 - 0.280: 34 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+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 4.67e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+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 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.17e+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: 131 2.51 - 3.11: 11880 3.11 - 3.70: 26437 3.70 - 4.30: 41184 4.30 - 4.90: 64920 Nonbonded interactions: 144552 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144547 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.833 16299 Z= 0.724 Angle : 0.707 10.433 22004 Z= 0.453 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.563 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70717 (22004) hydrogen bonds : bond 0.16170 ( 896) hydrogen bonds : angle 6.35243 ( 2616) Misc. bond : bond 0.83345 ( 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 434 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 411 time to evaluate : 0.631 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: A 184 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8416 (tpp-160) REVERT: B 274 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7762 (ptp-110) outliers start: 23 outliers final: 6 residues processed: 427 average time/residue: 0.5842 time to fit residues: 273.0679 Evaluate side-chains 286 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 232 ASN A 668 ASN B 11 GLN B 14 ASN B 418 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096317 restraints weight = 20839.846| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.46 r_work: 0.2827 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16299 Z= 0.184 Angle : 0.586 10.770 22004 Z= 0.313 Chirality : 0.042 0.208 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.072 166.004 2228 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.92 % Allowed : 16.51 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 1928 helix: 1.73 (0.15), residues: 1125 sheet: 0.44 (0.41), residues: 132 loop : 0.67 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.020 0.001 TYR D 105 PHE 0.022 0.002 PHE B 624 TRP 0.012 0.002 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00410 (16298) covalent geometry : angle 0.58629 (22004) hydrogen bonds : bond 0.04380 ( 896) hydrogen bonds : angle 4.92051 ( 2616) Misc. bond : bond 0.00016 ( 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 364 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 184 ARG cc_start: 0.9191 (tpp-160) cc_final: 0.8860 (tpp-160) REVERT: A 194 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8982 (tttm) REVERT: A 232 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8584 (m-40) REVERT: A 246 SER cc_start: 0.8172 (m) cc_final: 0.7686 (p) REVERT: A 274 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8300 (ttt90) REVERT: A 276 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8926 (mmpt) REVERT: A 296 LYS cc_start: 0.8784 (mttt) cc_final: 0.8221 (mmmt) REVERT: A 602 GLU cc_start: 0.8982 (tt0) cc_final: 0.8289 (tt0) REVERT: A 604 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8508 (mmt90) REVERT: B 11 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: B 15 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8521 (mm-30) REVERT: B 52 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9142 (tptm) REVERT: B 56 ASP cc_start: 0.9164 (m-30) cc_final: 0.8863 (m-30) REVERT: B 79 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 112 LYS cc_start: 0.9313 (mtpp) cc_final: 0.9092 (mtmm) REVERT: B 120 ASP cc_start: 0.8985 (m-30) cc_final: 0.8734 (m-30) REVERT: B 235 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8844 (mtm-85) REVERT: B 274 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7077 (ptp90) REVERT: B 276 LYS cc_start: 0.8994 (ptpp) cc_final: 0.8729 (mmtm) REVERT: B 341 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.9009 (mmmm) REVERT: B 343 LEU cc_start: 0.9386 (mt) cc_final: 0.9148 (mt) REVERT: B 402 GLU cc_start: 0.8959 (tp30) cc_final: 0.8707 (mp0) REVERT: B 603 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 604 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8926 (mmp80) REVERT: B 610 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8419 (mtpp) REVERT: B 659 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8321 (mtpp) REVERT: C 56 MET cc_start: -0.0554 (mmp) cc_final: -0.1012 (tpt) REVERT: C 129 LYS cc_start: 0.3980 (tptt) cc_final: 0.3775 (tptt) REVERT: C 287 LEU cc_start: 0.0088 (OUTLIER) cc_final: -0.0140 (pp) outliers start: 50 outliers final: 9 residues processed: 343 average time/residue: 0.7362 time to fit residues: 275.8217 Evaluate side-chains 283 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 668 ASN B 109 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.185393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096774 restraints weight = 21162.924| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.38 r_work: 0.2833 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16299 Z= 0.159 Angle : 0.548 10.882 22004 Z= 0.290 Chirality : 0.041 0.179 2348 Planarity : 0.003 0.054 2812 Dihedral : 8.702 162.728 2217 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.09 % Allowed : 17.09 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 1928 helix: 1.71 (0.15), residues: 1137 sheet: 0.12 (0.40), residues: 140 loop : 0.73 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.018 0.001 TYR C 46 PHE 0.016 0.001 PHE B 261 TRP 0.009 0.001 TRP A 9 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00356 (16298) covalent geometry : angle 0.54751 (22004) hydrogen bonds : bond 0.03923 ( 896) hydrogen bonds : angle 4.74805 ( 2616) Misc. bond : bond 0.00033 ( 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 331 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.655 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 79 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 178 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9075 (p) REVERT: A 184 ARG cc_start: 0.9097 (tpp-160) cc_final: 0.8735 (tpp-160) REVERT: A 194 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8942 (tttm) REVERT: A 246 SER cc_start: 0.8006 (m) cc_final: 0.7497 (p) REVERT: A 274 ARG cc_start: 0.8632 (ttt90) cc_final: 0.8153 (ttt90) REVERT: A 276 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8735 (mmpt) REVERT: A 296 LYS cc_start: 0.8784 (mttt) cc_final: 0.8170 (mmmt) REVERT: A 444 ASP cc_start: 0.8643 (t70) cc_final: 0.8215 (p0) REVERT: A 602 GLU cc_start: 0.8920 (tt0) cc_final: 0.8624 (tt0) REVERT: B 15 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8489 (mm-30) REVERT: B 31 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9124 (mt-10) REVERT: B 52 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9088 (tptm) REVERT: B 56 ASP cc_start: 0.9117 (m-30) cc_final: 0.8797 (m-30) REVERT: B 99 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8861 (tppt) REVERT: B 120 ASP cc_start: 0.8985 (m-30) cc_final: 0.8679 (m-30) REVERT: B 194 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8997 (ptmt) REVERT: B 232 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8371 (m-40) REVERT: B 235 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8649 (mtm-85) REVERT: B 274 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7331 (ptp90) REVERT: B 341 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8968 (mmmm) REVERT: B 343 LEU cc_start: 0.9335 (mt) cc_final: 0.9061 (mt) REVERT: B 362 ASP cc_start: 0.8718 (m-30) cc_final: 0.8308 (m-30) REVERT: B 603 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 604 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8937 (mmp80) REVERT: B 610 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8549 (mtpp) REVERT: B 659 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8196 (mtpp) REVERT: C 287 LEU cc_start: 0.0311 (OUTLIER) cc_final: 0.0104 (pt) REVERT: D 103 LYS cc_start: 0.5274 (tptm) cc_final: 0.4913 (pptt) outliers start: 53 outliers final: 17 residues processed: 307 average time/residue: 0.7541 time to fit residues: 252.7370 Evaluate side-chains 283 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 50.0000 chunk 132 optimal weight: 0.9980 chunk 185 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 172 optimal weight: 40.0000 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 40.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN B 11 GLN B 232 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092364 restraints weight = 21094.815| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.36 r_work: 0.2756 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16299 Z= 0.309 Angle : 0.602 10.971 22004 Z= 0.319 Chirality : 0.044 0.169 2348 Planarity : 0.004 0.048 2812 Dihedral : 9.010 167.697 2217 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.91 % Allowed : 16.86 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 1928 helix: 1.60 (0.15), residues: 1134 sheet: -0.05 (0.42), residues: 128 loop : 0.60 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 446 TYR 0.034 0.002 TYR D 105 PHE 0.018 0.002 PHE A 492 TRP 0.011 0.001 TRP B 9 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00702 (16298) covalent geometry : angle 0.60236 (22004) hydrogen bonds : bond 0.04070 ( 896) hydrogen bonds : angle 4.80171 ( 2616) Misc. bond : bond 0.00067 ( 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 315 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 184 ARG cc_start: 0.9203 (tpp-160) cc_final: 0.8928 (tpp-160) REVERT: A 274 ARG cc_start: 0.8593 (ttt90) cc_final: 0.8176 (ttt90) REVERT: A 316 GLU cc_start: 0.8577 (tp30) cc_final: 0.8345 (tp30) REVERT: A 444 ASP cc_start: 0.8614 (t70) cc_final: 0.8131 (p0) REVERT: A 602 GLU cc_start: 0.8992 (tt0) cc_final: 0.8784 (tt0) REVERT: B 11 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: B 15 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8549 (mp0) REVERT: B 52 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9096 (tptm) REVERT: B 56 ASP cc_start: 0.9132 (m-30) cc_final: 0.8793 (m-30) REVERT: B 79 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 99 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8989 (tppt) REVERT: B 112 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9085 (mtmm) REVERT: B 228 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8834 (mtmt) REVERT: B 232 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8495 (m110) REVERT: B 274 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8288 (ptm160) REVERT: B 341 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8996 (mmmm) REVERT: B 402 GLU cc_start: 0.8990 (tp30) cc_final: 0.8672 (mp0) REVERT: B 603 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 604 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8905 (mmp80) REVERT: B 610 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8648 (mtpp) REVERT: B 659 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: C 56 MET cc_start: -0.0504 (mmp) cc_final: -0.1025 (tpt) REVERT: D 103 LYS cc_start: 0.5289 (tptm) cc_final: 0.4952 (pptt) REVERT: D 269 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5592 (mpm) outliers start: 67 outliers final: 26 residues processed: 291 average time/residue: 0.7422 time to fit residues: 235.9036 Evaluate side-chains 274 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 164 optimal weight: 40.0000 chunk 189 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.096971 restraints weight = 21048.572| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.38 r_work: 0.2844 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16299 Z= 0.136 Angle : 0.538 11.756 22004 Z= 0.283 Chirality : 0.040 0.191 2348 Planarity : 0.003 0.045 2812 Dihedral : 8.564 162.635 2217 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.57 % Allowed : 18.38 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.19), residues: 1928 helix: 1.65 (0.15), residues: 1134 sheet: -0.26 (0.40), residues: 140 loop : 0.63 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 446 TYR 0.014 0.001 TYR C 46 PHE 0.027 0.001 PHE B 624 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00301 (16298) covalent geometry : angle 0.53753 (22004) hydrogen bonds : bond 0.03585 ( 896) hydrogen bonds : angle 4.61722 ( 2616) Misc. bond : bond 0.00758 ( 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 305 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 184 ARG cc_start: 0.9158 (tpp-160) cc_final: 0.8802 (tpp-160) REVERT: A 274 ARG cc_start: 0.8647 (ttt90) cc_final: 0.7863 (ttm170) REVERT: A 276 LYS cc_start: 0.9133 (mtpp) cc_final: 0.8738 (mmpt) REVERT: A 316 GLU cc_start: 0.8589 (tp30) cc_final: 0.8371 (tp30) REVERT: A 402 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8433 (mt-10) REVERT: A 441 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8614 (mm-30) REVERT: A 444 ASP cc_start: 0.8658 (t70) cc_final: 0.8044 (p0) REVERT: A 589 SER cc_start: 0.9626 (t) cc_final: 0.9334 (t) REVERT: A 602 GLU cc_start: 0.8895 (tt0) cc_final: 0.8662 (tt0) REVERT: B 11 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: B 15 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8542 (mm-30) REVERT: B 52 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9103 (tptm) REVERT: B 56 ASP cc_start: 0.9046 (m-30) cc_final: 0.8751 (m-30) REVERT: B 79 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 120 ASP cc_start: 0.8995 (m-30) cc_final: 0.8758 (m-30) REVERT: B 194 LYS cc_start: 0.9222 (tttp) cc_final: 0.9011 (ptmt) REVERT: B 228 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8764 (mtmt) REVERT: B 274 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7388 (ptp90) REVERT: B 335 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 341 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8988 (mmmm) REVERT: B 343 LEU cc_start: 0.9330 (mt) cc_final: 0.9081 (mt) REVERT: B 362 ASP cc_start: 0.8751 (m-30) cc_final: 0.8355 (m-30) REVERT: B 402 GLU cc_start: 0.8997 (tp30) cc_final: 0.8709 (mp0) REVERT: B 603 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8062 (tm-30) REVERT: B 604 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8792 (mmp80) REVERT: B 610 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8482 (mtpp) REVERT: B 659 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8221 (mtpp) REVERT: B 686 ARG cc_start: 0.8324 (mtp85) cc_final: 0.8065 (mtp85) REVERT: C 287 LEU cc_start: 0.0305 (OUTLIER) cc_final: 0.0103 (pp) REVERT: D 46 TYR cc_start: 0.8542 (m-10) cc_final: 0.8239 (p90) REVERT: D 269 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5916 (mpm) outliers start: 44 outliers final: 17 residues processed: 285 average time/residue: 0.7725 time to fit residues: 240.0502 Evaluate side-chains 267 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 0.0170 chunk 125 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 11 GLN B 62 GLN ** B 232 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 = 0.4140 r_free = 0.4140 target = 0.186846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099674 restraints weight = 20884.744| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.36 r_work: 0.2907 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16299 Z= 0.114 Angle : 0.527 12.552 22004 Z= 0.276 Chirality : 0.039 0.181 2348 Planarity : 0.003 0.053 2812 Dihedral : 8.069 157.085 2217 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.93 % Allowed : 20.19 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 1928 helix: 1.77 (0.15), residues: 1131 sheet: 0.08 (0.42), residues: 128 loop : 0.45 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 446 TYR 0.035 0.001 TYR D 105 PHE 0.015 0.001 PHE A 492 TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00244 (16298) covalent geometry : angle 0.52730 (22004) hydrogen bonds : bond 0.03341 ( 896) hydrogen bonds : angle 4.47301 ( 2616) Misc. bond : bond 0.00060 ( 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 309 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8971 (ptpp) REVERT: A 178 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.9095 (p) REVERT: A 232 ASN cc_start: 0.9081 (m-40) cc_final: 0.8813 (m110) REVERT: A 274 ARG cc_start: 0.8684 (ttt90) cc_final: 0.8300 (ttm170) REVERT: A 276 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8840 (mmmt) REVERT: A 296 LYS cc_start: 0.8798 (mttt) cc_final: 0.8204 (mmmt) REVERT: A 402 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8414 (mt-10) REVERT: A 444 ASP cc_start: 0.8640 (t70) cc_final: 0.8057 (p0) REVERT: A 589 SER cc_start: 0.9642 (t) cc_final: 0.9344 (t) REVERT: A 599 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8851 (mt-10) REVERT: A 602 GLU cc_start: 0.8874 (tt0) cc_final: 0.8505 (tt0) REVERT: A 604 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8507 (mmt-90) REVERT: A 686 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7964 (mtp85) REVERT: B 15 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 52 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9114 (tptm) REVERT: B 56 ASP cc_start: 0.8994 (m-30) cc_final: 0.8704 (m-30) REVERT: B 79 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 120 ASP cc_start: 0.8925 (m-30) cc_final: 0.8673 (m-30) REVERT: B 184 ARG cc_start: 0.9246 (tpp-160) cc_final: 0.9012 (tpp-160) REVERT: B 274 ARG cc_start: 0.8433 (ptm160) cc_final: 0.7296 (ptp90) REVERT: B 296 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8659 (ptpp) REVERT: B 335 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 341 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8948 (mmmm) REVERT: B 343 LEU cc_start: 0.9341 (mt) cc_final: 0.9094 (mt) REVERT: B 362 ASP cc_start: 0.8620 (m-30) cc_final: 0.8236 (m-30) REVERT: B 396 ASP cc_start: 0.8725 (m-30) cc_final: 0.8372 (m-30) REVERT: B 526 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8402 (mp0) REVERT: B 604 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8853 (mmp80) REVERT: B 610 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8448 (mtpp) REVERT: B 655 THR cc_start: 0.9290 (m) cc_final: 0.9072 (t) REVERT: B 668 ASN cc_start: 0.9264 (m-40) cc_final: 0.9053 (m110) REVERT: D 46 TYR cc_start: 0.8492 (m-10) cc_final: 0.8188 (p90) REVERT: D 269 MET cc_start: 0.6141 (mpp) cc_final: 0.5906 (mpm) outliers start: 33 outliers final: 12 residues processed: 295 average time/residue: 0.7239 time to fit residues: 234.4258 Evaluate side-chains 273 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 50.0000 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.183100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095178 restraints weight = 20784.458| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.31 r_work: 0.2821 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16299 Z= 0.218 Angle : 0.581 13.294 22004 Z= 0.303 Chirality : 0.042 0.170 2348 Planarity : 0.003 0.042 2812 Dihedral : 8.297 163.796 2216 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.28 % Allowed : 20.60 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 1928 helix: 1.67 (0.15), residues: 1132 sheet: -0.51 (0.39), residues: 144 loop : 0.61 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 350 TYR 0.027 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00496 (16298) covalent geometry : angle 0.58129 (22004) hydrogen bonds : bond 0.03626 ( 896) hydrogen bonds : angle 4.60849 ( 2616) Misc. bond : bond 0.00088 ( 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 288 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8812 (tptt) REVERT: A 112 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9043 (ptpp) REVERT: A 214 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7717 (mttp) REVERT: A 274 ARG cc_start: 0.8726 (ttt90) cc_final: 0.8432 (ttm-80) REVERT: A 276 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8727 (mmpt) REVERT: A 296 LYS cc_start: 0.8789 (mttt) cc_final: 0.8167 (mmmt) REVERT: A 402 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8478 (mm-30) REVERT: A 444 ASP cc_start: 0.8595 (t70) cc_final: 0.8002 (p0) REVERT: A 589 SER cc_start: 0.9623 (t) cc_final: 0.9368 (t) REVERT: A 602 GLU cc_start: 0.8878 (tt0) cc_final: 0.8236 (tt0) REVERT: A 604 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8207 (mmt-90) REVERT: B 52 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9114 (tptm) REVERT: B 56 ASP cc_start: 0.9038 (m-30) cc_final: 0.8743 (m-30) REVERT: B 79 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 112 LYS cc_start: 0.9315 (mtpp) cc_final: 0.9053 (mtpm) REVERT: B 120 ASP cc_start: 0.9045 (m-30) cc_final: 0.8792 (m-30) REVERT: B 274 ARG cc_start: 0.8472 (ptm160) cc_final: 0.7717 (ttm110) REVERT: B 335 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 341 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (mmmm) REVERT: B 343 LEU cc_start: 0.9363 (mt) cc_final: 0.9100 (mt) REVERT: B 362 ASP cc_start: 0.8722 (m-30) cc_final: 0.8367 (m-30) REVERT: B 396 ASP cc_start: 0.8774 (m-30) cc_final: 0.8497 (m-30) REVERT: B 402 GLU cc_start: 0.8964 (tp30) cc_final: 0.8717 (mp0) REVERT: B 604 ARG cc_start: 0.9266 (mmp80) cc_final: 0.8763 (mmp80) REVERT: B 610 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8270 (ttpp) REVERT: B 659 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8303 (mtpp) REVERT: C 319 ASP cc_start: 0.9216 (m-30) cc_final: 0.8907 (m-30) REVERT: D 105 TYR cc_start: 0.2439 (OUTLIER) cc_final: 0.1576 (p90) REVERT: D 269 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5933 (mmp) outliers start: 39 outliers final: 20 residues processed: 268 average time/residue: 0.7571 time to fit residues: 221.2863 Evaluate side-chains 264 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095900 restraints weight = 20982.556| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.35 r_work: 0.2835 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16299 Z= 0.181 Angle : 0.580 15.148 22004 Z= 0.301 Chirality : 0.041 0.171 2348 Planarity : 0.003 0.041 2812 Dihedral : 8.224 162.834 2216 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.98 % Allowed : 20.89 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1134 sheet: -0.54 (0.40), residues: 144 loop : 0.61 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 350 TYR 0.023 0.001 TYR D 105 PHE 0.018 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00411 (16298) covalent geometry : angle 0.57998 (22004) hydrogen bonds : bond 0.03506 ( 896) hydrogen bonds : angle 4.56106 ( 2616) Misc. bond : bond 0.00169 ( 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 287 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.652 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: A 30 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8793 (tptt) REVERT: A 112 LYS cc_start: 0.9285 (mtpp) cc_final: 0.9061 (ptpp) REVERT: A 232 ASN cc_start: 0.9084 (m-40) cc_final: 0.8799 (m110) REVERT: A 274 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8380 (ttm170) REVERT: A 276 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8770 (mmtt) REVERT: A 402 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8519 (mm-30) REVERT: A 444 ASP cc_start: 0.8690 (t70) cc_final: 0.8256 (p0) REVERT: A 452 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8659 (ttt90) REVERT: A 589 SER cc_start: 0.9632 (t) cc_final: 0.9368 (t) REVERT: B 15 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 52 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9103 (tptm) REVERT: B 56 ASP cc_start: 0.9043 (m-30) cc_final: 0.8745 (m-30) REVERT: B 79 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 112 LYS cc_start: 0.9301 (mtpp) cc_final: 0.9049 (mtpm) REVERT: B 120 ASP cc_start: 0.9040 (m-30) cc_final: 0.8785 (m-30) REVERT: B 274 ARG cc_start: 0.8397 (ptm160) cc_final: 0.7363 (ptp90) REVERT: B 335 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 341 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8969 (mmmm) REVERT: B 343 LEU cc_start: 0.9380 (mt) cc_final: 0.9119 (mt) REVERT: B 362 ASP cc_start: 0.8733 (m-30) cc_final: 0.8382 (m-30) REVERT: B 396 ASP cc_start: 0.8853 (m-30) cc_final: 0.8577 (m-30) REVERT: B 402 GLU cc_start: 0.9009 (tp30) cc_final: 0.8753 (mp0) REVERT: B 526 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8434 (mp0) REVERT: B 604 ARG cc_start: 0.9217 (mmp80) cc_final: 0.8832 (mmp80) REVERT: C 56 MET cc_start: -0.1045 (tpp) cc_final: -0.1311 (tpt) REVERT: C 319 ASP cc_start: 0.9232 (m-30) cc_final: 0.8959 (m-30) REVERT: D 105 TYR cc_start: 0.2203 (OUTLIER) cc_final: 0.1285 (p90) REVERT: D 269 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6165 (mmp) outliers start: 34 outliers final: 21 residues processed: 269 average time/residue: 0.7608 time to fit residues: 224.2769 Evaluate side-chains 261 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 143 optimal weight: 50.0000 chunk 28 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097757 restraints weight = 20947.182| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.34 r_work: 0.2842 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16299 Z= 0.171 Angle : 0.597 17.363 22004 Z= 0.307 Chirality : 0.041 0.194 2348 Planarity : 0.003 0.038 2812 Dihedral : 8.201 163.180 2216 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.75 % Allowed : 21.53 % 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 aren not related in a simple way. whole: 1.64 (0.19), residues: 1928 helix: 1.67 (0.15), residues: 1136 sheet: -0.58 (0.39), residues: 144 loop : 0.63 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.023 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00390 (16298) covalent geometry : angle 0.59674 (22004) hydrogen bonds : bond 0.03518 ( 896) hydrogen bonds : angle 4.56560 ( 2616) Misc. bond : bond 0.00138 ( 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 273 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.702 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: A 30 LYS cc_start: 0.9262 (ttmm) cc_final: 0.8793 (tptt) REVERT: A 112 LYS cc_start: 0.9271 (mtpp) cc_final: 0.9042 (ptpp) REVERT: A 232 ASN cc_start: 0.9035 (m-40) cc_final: 0.8750 (m110) REVERT: A 274 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8364 (ttm170) REVERT: A 276 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8725 (mmtt) REVERT: A 402 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 444 ASP cc_start: 0.8794 (t70) cc_final: 0.8302 (p0) REVERT: A 452 ARG cc_start: 0.9029 (ttp80) cc_final: 0.8676 (ttt90) REVERT: A 589 SER cc_start: 0.9630 (t) cc_final: 0.9363 (t) REVERT: A 604 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8340 (mmt-90) REVERT: B 52 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9113 (tptm) REVERT: B 56 ASP cc_start: 0.9057 (m-30) cc_final: 0.8755 (m-30) REVERT: B 79 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 112 LYS cc_start: 0.9318 (mtpp) cc_final: 0.9061 (mtpm) REVERT: B 120 ASP cc_start: 0.9046 (m-30) cc_final: 0.8776 (m-30) REVERT: B 246 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7734 (p) REVERT: B 274 ARG cc_start: 0.8353 (ptm160) cc_final: 0.7317 (ptp90) REVERT: B 335 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 341 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8961 (mmmm) REVERT: B 343 LEU cc_start: 0.9377 (mt) cc_final: 0.9116 (mt) REVERT: B 362 ASP cc_start: 0.8737 (m-30) cc_final: 0.8366 (m-30) REVERT: B 396 ASP cc_start: 0.8836 (m-30) cc_final: 0.8575 (m-30) REVERT: B 402 GLU cc_start: 0.8998 (tp30) cc_final: 0.8708 (mp0) REVERT: B 526 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8450 (mp0) REVERT: B 604 ARG cc_start: 0.9148 (mmp80) cc_final: 0.8766 (mmp80) REVERT: B 659 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8337 (mtpp) REVERT: C 56 MET cc_start: -0.1009 (tpp) cc_final: -0.1223 (tpt) REVERT: C 74 MET cc_start: 0.2119 (mpm) cc_final: 0.1833 (mmm) REVERT: C 317 ASP cc_start: 0.9131 (m-30) cc_final: 0.8391 (t0) REVERT: D 46 TYR cc_start: 0.8473 (m-10) cc_final: 0.8125 (p90) REVERT: D 105 TYR cc_start: 0.2207 (OUTLIER) cc_final: 0.1250 (p90) REVERT: D 269 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6195 (mmp) outliers start: 30 outliers final: 17 residues processed: 259 average time/residue: 0.7551 time to fit residues: 213.8794 Evaluate side-chains 263 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.187166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099928 restraints weight = 21022.590| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.40 r_work: 0.2868 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16299 Z= 0.146 Angle : 0.590 18.322 22004 Z= 0.305 Chirality : 0.040 0.180 2348 Planarity : 0.003 0.039 2812 Dihedral : 8.048 161.937 2216 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % Rotamer: Outliers : 1.75 % Allowed : 21.76 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1134 sheet: -0.56 (0.40), residues: 148 loop : 0.60 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 446 TYR 0.023 0.001 TYR D 105 PHE 0.032 0.001 PHE B 624 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00332 (16298) covalent geometry : angle 0.59028 (22004) hydrogen bonds : bond 0.03387 ( 896) hydrogen bonds : angle 4.54030 ( 2616) Misc. bond : bond 0.00118 ( 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 291 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.550 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 30 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8727 (tptt) REVERT: A 112 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8982 (ptpp) REVERT: A 194 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8827 (tttm) REVERT: A 274 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8426 (ttm170) REVERT: A 276 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8697 (mmtt) REVERT: A 296 LYS cc_start: 0.8690 (mttt) cc_final: 0.8039 (mmmt) REVERT: A 402 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8451 (mm-30) REVERT: A 441 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8571 (mt-10) REVERT: A 444 ASP cc_start: 0.8793 (t70) cc_final: 0.8326 (p0) REVERT: A 452 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8584 (ttt90) REVERT: A 589 SER cc_start: 0.9619 (t) cc_final: 0.9362 (t) REVERT: A 604 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8311 (mmt-90) REVERT: A 686 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7915 (mtp85) REVERT: B 52 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9105 (tptm) REVERT: B 56 ASP cc_start: 0.9037 (m-30) cc_final: 0.8771 (m-30) REVERT: B 79 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 112 LYS cc_start: 0.9306 (mtpp) cc_final: 0.9028 (mtpm) REVERT: B 120 ASP cc_start: 0.9021 (m-30) cc_final: 0.8746 (m-30) REVERT: B 246 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7690 (p) REVERT: B 274 ARG cc_start: 0.8301 (ptm160) cc_final: 0.7288 (ptp90) REVERT: B 296 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8581 (ptpp) REVERT: B 335 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 341 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8920 (mmmm) REVERT: B 343 LEU cc_start: 0.9322 (mt) cc_final: 0.9049 (mt) REVERT: B 362 ASP cc_start: 0.8631 (m-30) cc_final: 0.8233 (m-30) REVERT: B 396 ASP cc_start: 0.8673 (m-30) cc_final: 0.8335 (m-30) REVERT: B 598 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8808 (mmm) REVERT: B 604 ARG cc_start: 0.9052 (mmp80) cc_final: 0.8739 (mmp80) REVERT: C 56 MET cc_start: -0.1015 (tpp) cc_final: -0.1221 (tpt) REVERT: C 74 MET cc_start: 0.1887 (mpm) cc_final: 0.1551 (mmm) REVERT: C 317 ASP cc_start: 0.9120 (m-30) cc_final: 0.8366 (t0) REVERT: D 46 TYR cc_start: 0.8481 (m-10) cc_final: 0.8172 (p90) REVERT: D 105 TYR cc_start: 0.2237 (OUTLIER) cc_final: 0.1322 (p90) REVERT: D 269 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6269 (mmp) outliers start: 30 outliers final: 17 residues processed: 276 average time/residue: 0.6718 time to fit residues: 203.1462 Evaluate side-chains 268 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 269 MET 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: 0.7980 chunk 151 optimal weight: 40.0000 chunk 162 optimal weight: 0.6980 chunk 146 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 312 GLN A 668 ASN B 232 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.187021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100581 restraints weight = 20939.252| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.35 r_work: 0.2884 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16299 Z= 0.139 Angle : 0.589 18.205 22004 Z= 0.303 Chirality : 0.040 0.168 2348 Planarity : 0.003 0.060 2812 Dihedral : 7.861 161.664 2216 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.98 % Allowed : 21.82 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.19), residues: 1928 helix: 1.71 (0.15), residues: 1135 sheet: -0.51 (0.40), residues: 148 loop : 0.60 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 686 TYR 0.022 0.001 TYR D 105 PHE 0.018 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00316 (16298) covalent geometry : angle 0.58897 (22004) hydrogen bonds : bond 0.03324 ( 896) hydrogen bonds : angle 4.49348 ( 2616) Misc. bond : bond 0.00093 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10241.51 seconds wall clock time: 174 minutes 53.33 seconds (10493.33 seconds total)