Starting phenix.real_space_refine on Thu Aug 6 17:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2026/9bxx_45014.cif" } resolution = 4.26 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 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10641 2.51 5 N 2712 2.21 5 O 3216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 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: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.64, per 1000 atoms: 0.16 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 139.932, 145.002, 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 87 16.00 P 16 15.00 Mg 2 11.99 O 3216 8.00 N 2712 7.00 C 10641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 437.9 milliseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.260A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.788A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) 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 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A 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 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A 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 367 removed outlier: 4.232A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.568A 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 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A 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 40 removed outlier: 3.613A 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 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.634A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.880A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.235A 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 removed outlier: 3.513A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A 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 588 removed outlier: 4.255A 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 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A 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: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A 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 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.233A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.022A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (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 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.818A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (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 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.468A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2664 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: 2.47 Time building geometry restraints manager: 1.46 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: 5044 1.34 - 1.46: 3105 1.46 - 1.58: 8700 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17038 Sorted by residual: bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " ideal model delta sigma weight residual 1.748 1.611 0.137 2.00e-02 2.50e+03 4.66e+01 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 2.40e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3A TTP B 802 " pdb=" PB TTP B 802 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22197 2.09 - 4.19: 711 4.19 - 6.28: 87 6.28 - 8.37: 17 8.37 - 10.46: 8 Bond angle restraints: 23020 Sorted by residual: angle pdb=" C VAL E 69 " pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " ideal model delta sigma weight residual 111.15 119.33 -8.18 1.30e+00 5.92e-01 3.96e+01 angle pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " pdb=" CG1 VAL E 69 " ideal model delta sigma weight residual 110.40 118.71 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.50 -4.31 1.06e+00 8.90e-01 1.65e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 9482 26.14 - 52.28: 701 52.28 - 78.41: 105 78.41 - 104.55: 14 104.55 - 130.69: 2 Dihedral angle restraints: 10304 sinusoidal: 4312 harmonic: 5992 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.28 84.28 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" O4' GDP A 804 " pdb=" C1' GDP A 804 " pdb=" N9 GDP A 804 " pdb=" C8 GDP A 804 " ideal model delta sinusoidal sigma weight residual 27.02 -103.67 130.69 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -101.11 128.13 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2219 0.093 - 0.186: 207 0.186 - 0.280: 33 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2464 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 5.43e+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 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.078 2.00e-02 2.50e+03 3.70e-02 3.43e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.041 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP B 623 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 124 2.51 - 3.11: 12002 3.11 - 3.70: 27791 3.70 - 4.30: 42534 4.30 - 4.90: 68522 Nonbonded interactions: 150973 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150968 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.310 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 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 0.630 17041 Z= 0.430 Angle : 0.869 13.547 23026 Z= 0.524 Chirality : 0.059 0.466 2464 Planarity : 0.004 0.041 2931 Dihedral : 17.518 130.690 6447 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 16.27 % Favored : 82.34 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.31 (0.37), residues: 179 loop : 0.43 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.029 0.002 TYR E 67 PHE 0.021 0.002 PHE D 92 TRP 0.078 0.006 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.36 (17038) covalent geometry : angle 0.86383 / 0.52 (23020) SS BOND : bond 0.36353 / 13.46 ( 3) SS BOND : angle 6.09121 / 3.51 ( 6) hydrogen bonds : bond 0.16740 / 11.21 ( 912) hydrogen bonds : angle 6.70338 / 4.60 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 863 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8493 (mt) cc_final: 0.8243 (mm) REVERT: A 99 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8873 (mmmm) REVERT: A 147 GLN cc_start: 0.8226 (mt0) cc_final: 0.7776 (mt0) REVERT: A 181 ASP cc_start: 0.8683 (m-30) cc_final: 0.8333 (m-30) REVERT: A 188 ILE cc_start: 0.8849 (mt) cc_final: 0.8432 (mt) REVERT: A 213 ILE cc_start: 0.7163 (mt) cc_final: 0.6951 (tp) REVERT: A 216 VAL cc_start: 0.8023 (p) cc_final: 0.7802 (m) REVERT: A 257 ASP cc_start: 0.8033 (m-30) cc_final: 0.7790 (m-30) REVERT: A 466 MET cc_start: 0.6595 (ptt) cc_final: 0.6350 (ptt) REVERT: A 493 MET cc_start: 0.8059 (tmm) cc_final: 0.7835 (tmm) REVERT: A 500 ILE cc_start: 0.9119 (mt) cc_final: 0.8752 (mt) REVERT: A 501 GLN cc_start: 0.8436 (tt0) cc_final: 0.8065 (tt0) REVERT: A 506 ILE cc_start: 0.8783 (mt) cc_final: 0.8354 (mt) REVERT: A 553 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: A 594 VAL cc_start: 0.8429 (m) cc_final: 0.8164 (m) REVERT: A 630 TYR cc_start: 0.6513 (m-80) cc_final: 0.5058 (m-80) REVERT: A 644 ILE cc_start: 0.9047 (mt) cc_final: 0.8674 (mt) REVERT: B 68 PHE cc_start: 0.8403 (p90) cc_final: 0.7992 (p90) REVERT: B 69 LEU cc_start: 0.8205 (mt) cc_final: 0.7921 (mt) REVERT: B 87 LYS cc_start: 0.8400 (tptp) cc_final: 0.8112 (tptp) REVERT: B 172 LEU cc_start: 0.8956 (mp) cc_final: 0.8645 (mp) REVERT: B 175 VAL cc_start: 0.9060 (t) cc_final: 0.8839 (t) REVERT: B 204 SER cc_start: 0.8686 (m) cc_final: 0.7745 (t) REVERT: B 257 ASP cc_start: 0.8565 (m-30) cc_final: 0.7956 (m-30) REVERT: B 258 ILE cc_start: 0.8603 (tp) cc_final: 0.8400 (tp) REVERT: B 277 THR cc_start: 0.7976 (p) cc_final: 0.7405 (p) REVERT: B 322 MET cc_start: 0.7121 (mmm) cc_final: 0.6280 (mmm) REVERT: B 349 LEU cc_start: 0.8910 (mt) cc_final: 0.8697 (mt) REVERT: B 391 VAL cc_start: 0.9041 (p) cc_final: 0.8766 (p) REVERT: B 468 LEU cc_start: 0.8582 (tp) cc_final: 0.8342 (tp) REVERT: B 472 LEU cc_start: 0.8818 (mt) cc_final: 0.8457 (mt) REVERT: B 493 MET cc_start: 0.7793 (tmm) cc_final: 0.7573 (tmm) REVERT: B 550 MET cc_start: 0.7183 (mtm) cc_final: 0.6876 (mtp) REVERT: B 565 VAL cc_start: 0.9021 (t) cc_final: 0.8609 (m) REVERT: B 574 TYR cc_start: 0.7844 (m-80) cc_final: 0.7504 (m-80) REVERT: B 575 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7342 (mtm-85) REVERT: B 576 LEU cc_start: 0.8791 (mt) cc_final: 0.8411 (mt) REVERT: B 589 SER cc_start: 0.8776 (m) cc_final: 0.8316 (m) REVERT: B 645 GLN cc_start: 0.8022 (tp40) cc_final: 0.7685 (tp40) REVERT: B 658 LEU cc_start: 0.8882 (mt) cc_final: 0.8638 (mp) REVERT: B 664 THR cc_start: 0.8929 (p) cc_final: 0.8567 (t) REVERT: C 33 GLU cc_start: 0.1905 (mp0) cc_final: 0.1276 (tm-30) REVERT: C 153 LEU cc_start: 0.6439 (tp) cc_final: 0.6109 (tp) REVERT: C 201 HIS cc_start: 0.3596 (m170) cc_final: 0.2465 (m170) REVERT: C 316 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6705 (mtmm) REVERT: D 63 THR cc_start: 0.5201 (m) cc_final: 0.4949 (m) REVERT: D 286 VAL cc_start: 0.3482 (t) cc_final: 0.2962 (p) REVERT: E 78 LEU cc_start: 0.6809 (mp) cc_final: 0.6305 (mp) outliers start: 25 outliers final: 3 residues processed: 874 average time/residue: 0.1203 time to fit residues: 154.9433 Evaluate side-chains 577 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 573 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 232 ASN A 320 ASN A 370 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 61 ASN B 304 HIS B 447 ASN C 24 GLN C 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.152441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106115 restraints weight = 44894.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110230 restraints weight = 27325.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112957 restraints weight = 18243.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114726 restraints weight = 13629.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116000 restraints weight = 10947.628| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17041 Z= 0.262 Angle : 0.726 16.022 23026 Z= 0.384 Chirality : 0.045 0.234 2464 Planarity : 0.005 0.061 2931 Dihedral : 9.223 138.050 2373 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.34 % Allowed : 3.63 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2012 helix: 1.16 (0.15), residues: 1162 sheet: -0.39 (0.36), residues: 177 loop : 0.42 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.036 0.002 TYR B 36 PHE 0.028 0.003 PHE A 492 TRP 0.023 0.002 TRP B 558 HIS 0.009 0.002 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (17038) covalent geometry : angle 0.71419 / 0.38 (23020) SS BOND : bond 0.00742 / 0.35 ( 3) SS BOND : angle 7.94618 / 3.93 ( 6) hydrogen bonds : bond 0.05148 / 3.37 ( 912) hydrogen bonds : angle 5.30273 / 3.66 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 649 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.9357 (m-80) cc_final: 0.9096 (m-80) REVERT: A 99 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9317 (tppp) REVERT: A 147 GLN cc_start: 0.9171 (mt0) cc_final: 0.8624 (mt0) REVERT: A 186 ILE cc_start: 0.9541 (mm) cc_final: 0.9254 (mm) REVERT: A 190 MET cc_start: 0.9304 (mtm) cc_final: 0.8999 (mtm) REVERT: A 250 TYR cc_start: 0.7222 (m-80) cc_final: 0.6842 (m-80) REVERT: A 257 ASP cc_start: 0.8659 (m-30) cc_final: 0.8053 (m-30) REVERT: A 262 LEU cc_start: 0.9645 (mt) cc_final: 0.9429 (mt) REVERT: A 263 ASP cc_start: 0.9000 (m-30) cc_final: 0.8613 (m-30) REVERT: A 301 PHE cc_start: 0.8949 (m-80) cc_final: 0.8188 (m-10) REVERT: A 312 GLN cc_start: 0.8800 (tp40) cc_final: 0.8491 (tp40) REVERT: A 342 LEU cc_start: 0.9648 (tp) cc_final: 0.9441 (tp) REVERT: A 362 ASP cc_start: 0.8437 (m-30) cc_final: 0.7953 (m-30) REVERT: A 367 VAL cc_start: 0.9617 (m) cc_final: 0.9371 (p) REVERT: A 466 MET cc_start: 0.9045 (ptt) cc_final: 0.8737 (ptt) REVERT: A 467 ASN cc_start: 0.9013 (t0) cc_final: 0.8811 (t0) REVERT: A 475 ASN cc_start: 0.8883 (m-40) cc_final: 0.8566 (m110) REVERT: A 501 GLN cc_start: 0.9426 (tt0) cc_final: 0.8984 (tm-30) REVERT: A 516 GLN cc_start: 0.9252 (tt0) cc_final: 0.8814 (tt0) REVERT: A 571 TYR cc_start: 0.8643 (t80) cc_final: 0.8040 (t80) REVERT: A 628 GLU cc_start: 0.9254 (tt0) cc_final: 0.8965 (tt0) REVERT: A 632 MET cc_start: 0.8095 (mtt) cc_final: 0.7703 (mtt) REVERT: A 645 GLN cc_start: 0.8621 (tp40) cc_final: 0.8138 (tp40) REVERT: A 650 GLN cc_start: 0.8359 (mt0) cc_final: 0.7457 (mt0) REVERT: A 664 THR cc_start: 0.9336 (p) cc_final: 0.8824 (p) REVERT: A 668 ASN cc_start: 0.9026 (m-40) cc_final: 0.8418 (m-40) REVERT: A 686 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7040 (mmm160) REVERT: B 23 LYS cc_start: 0.9404 (mmtm) cc_final: 0.9003 (mmmt) REVERT: B 139 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8848 (mt-10) REVERT: B 144 MET cc_start: 0.9334 (mtm) cc_final: 0.8714 (mtm) REVERT: B 145 ILE cc_start: 0.9431 (tp) cc_final: 0.8975 (tp) REVERT: B 150 GLN cc_start: 0.9196 (tp40) cc_final: 0.8803 (tp-100) REVERT: B 172 LEU cc_start: 0.8826 (mp) cc_final: 0.8544 (mp) REVERT: B 184 ARG cc_start: 0.8861 (mtt180) cc_final: 0.8331 (ttm170) REVERT: B 186 ILE cc_start: 0.9713 (mt) cc_final: 0.9465 (mt) REVERT: B 190 MET cc_start: 0.9426 (mtm) cc_final: 0.8973 (mtm) REVERT: B 239 GLN cc_start: 0.7662 (mt0) cc_final: 0.7077 (mm-40) REVERT: B 250 TYR cc_start: 0.8322 (m-80) cc_final: 0.7940 (m-80) REVERT: B 274 ARG cc_start: 0.8122 (tmt-80) cc_final: 0.7821 (tpt90) REVERT: B 335 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 348 MET cc_start: 0.8553 (tpt) cc_final: 0.8265 (tpp) REVERT: B 375 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8138 (mmmm) REVERT: B 403 ILE cc_start: 0.9242 (mm) cc_final: 0.9009 (mm) REVERT: B 416 ILE cc_start: 0.9082 (mm) cc_final: 0.8783 (mm) REVERT: B 420 MET cc_start: 0.9038 (mmm) cc_final: 0.8711 (mmp) REVERT: B 477 ILE cc_start: 0.8610 (mm) cc_final: 0.8384 (mp) REVERT: B 496 ASN cc_start: 0.9403 (t0) cc_final: 0.8895 (t0) REVERT: B 500 ILE cc_start: 0.9407 (mt) cc_final: 0.9170 (mt) REVERT: B 501 GLN cc_start: 0.9535 (tt0) cc_final: 0.9246 (tt0) REVERT: B 576 LEU cc_start: 0.9253 (mt) cc_final: 0.9040 (mt) REVERT: B 586 TYR cc_start: 0.9506 (m-80) cc_final: 0.9195 (m-80) REVERT: B 604 ARG cc_start: 0.9312 (mmp80) cc_final: 0.8812 (mmp80) REVERT: B 640 MET cc_start: 0.9144 (tpp) cc_final: 0.8899 (tpp) REVERT: B 645 GLN cc_start: 0.9199 (tp40) cc_final: 0.8927 (tp-100) REVERT: B 650 GLN cc_start: 0.6643 (mt0) cc_final: 0.5904 (mt0) REVERT: B 686 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8123 (mmm160) REVERT: C 33 GLU cc_start: 0.4733 (mp0) cc_final: 0.4240 (pp20) REVERT: C 157 MET cc_start: 0.8602 (mtm) cc_final: 0.8111 (mtm) REVERT: C 162 TYR cc_start: 0.7814 (m-80) cc_final: 0.7586 (m-10) REVERT: C 177 TYR cc_start: 0.9000 (t80) cc_final: 0.8683 (t80) REVERT: D 82 ASP cc_start: 0.8820 (m-30) cc_final: 0.8463 (p0) REVERT: D 134 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8267 (mtmt) REVERT: D 137 MET cc_start: 0.5916 (ttt) cc_final: 0.5372 (tmm) REVERT: D 179 TYR cc_start: 0.8291 (t80) cc_final: 0.7993 (t80) REVERT: D 185 MET cc_start: 0.4385 (mmp) cc_final: 0.4057 (mpp) REVERT: D 242 TYR cc_start: 0.9081 (t80) cc_final: 0.8538 (t80) REVERT: D 262 TYR cc_start: 0.8684 (t80) cc_final: 0.8415 (t80) REVERT: D 269 MET cc_start: -0.3125 (mmp) cc_final: -0.3372 (mmp) outliers start: 6 outliers final: 2 residues processed: 651 average time/residue: 0.1176 time to fit residues: 116.3265 Evaluate side-chains 534 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 147 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 668 ASN C 132 GLN C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099302 restraints weight = 47015.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103035 restraints weight = 28845.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105531 restraints weight = 19720.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107255 restraints weight = 14744.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108376 restraints weight = 11818.157| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17041 Z= 0.292 Angle : 0.715 9.196 23026 Z= 0.379 Chirality : 0.046 0.192 2464 Planarity : 0.005 0.039 2931 Dihedral : 9.479 139.008 2373 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2012 helix: 0.77 (0.15), residues: 1168 sheet: 0.22 (0.40), residues: 147 loop : 0.04 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.029 0.002 TYR B 36 PHE 0.041 0.002 PHE C 92 TRP 0.017 0.002 TRP A 623 HIS 0.007 0.002 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 (17038) covalent geometry : angle 0.71183 / 0.38 (23020) SS BOND : bond 0.00591 / 0.31 ( 3) SS BOND : angle 4.09881 / 2.06 ( 6) hydrogen bonds : bond 0.04839 / 3.12 ( 912) hydrogen bonds : angle 5.30840 / 3.69 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 608 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.9494 (m-80) cc_final: 0.9174 (m-80) REVERT: A 186 ILE cc_start: 0.9571 (mm) cc_final: 0.9185 (mm) REVERT: A 190 MET cc_start: 0.9270 (mtm) cc_final: 0.8991 (mtm) REVERT: A 250 TYR cc_start: 0.7355 (m-80) cc_final: 0.6987 (m-80) REVERT: A 257 ASP cc_start: 0.8661 (m-30) cc_final: 0.8337 (m-30) REVERT: A 263 ASP cc_start: 0.8927 (m-30) cc_final: 0.8596 (m-30) REVERT: A 301 PHE cc_start: 0.8979 (m-80) cc_final: 0.8740 (m-10) REVERT: A 312 GLN cc_start: 0.8757 (tp40) cc_final: 0.8477 (tp40) REVERT: A 319 MET cc_start: 0.8975 (tpp) cc_final: 0.8747 (tmm) REVERT: A 322 MET cc_start: 0.8880 (mmm) cc_final: 0.8668 (mmm) REVERT: A 362 ASP cc_start: 0.8504 (m-30) cc_final: 0.8024 (m-30) REVERT: A 366 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8962 (ptpt) REVERT: A 447 ASN cc_start: 0.8638 (m-40) cc_final: 0.8381 (m-40) REVERT: A 475 ASN cc_start: 0.8982 (m-40) cc_final: 0.8741 (m110) REVERT: A 501 GLN cc_start: 0.9442 (tt0) cc_final: 0.9041 (tm-30) REVERT: A 571 TYR cc_start: 0.8851 (t80) cc_final: 0.8256 (t80) REVERT: A 588 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8846 (mm-40) REVERT: A 598 MET cc_start: 0.8545 (mtp) cc_final: 0.8091 (mtp) REVERT: A 599 GLU cc_start: 0.9055 (pt0) cc_final: 0.8808 (pt0) REVERT: A 601 ILE cc_start: 0.9512 (tt) cc_final: 0.9080 (tt) REVERT: A 615 MET cc_start: 0.8985 (mmp) cc_final: 0.8696 (mmp) REVERT: A 628 GLU cc_start: 0.9286 (tt0) cc_final: 0.8897 (tt0) REVERT: A 645 GLN cc_start: 0.8603 (tp40) cc_final: 0.8338 (tp40) REVERT: A 664 THR cc_start: 0.9438 (p) cc_final: 0.9004 (p) REVERT: A 668 ASN cc_start: 0.9055 (m-40) cc_final: 0.8768 (m-40) REVERT: A 669 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8423 (ttp-170) REVERT: A 686 ARG cc_start: 0.8376 (mmm160) cc_final: 0.7263 (mmm160) REVERT: B 10 ILE cc_start: 0.9722 (mt) cc_final: 0.9449 (tp) REVERT: B 23 LYS cc_start: 0.9434 (mmtm) cc_final: 0.9042 (mmmt) REVERT: B 106 LEU cc_start: 0.9144 (tp) cc_final: 0.8440 (tp) REVERT: B 167 LEU cc_start: 0.9102 (mt) cc_final: 0.8890 (mt) REVERT: B 172 LEU cc_start: 0.8927 (mp) cc_final: 0.8674 (mp) REVERT: B 184 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8553 (ttm-80) REVERT: B 190 MET cc_start: 0.9446 (mtm) cc_final: 0.9175 (mtm) REVERT: B 250 TYR cc_start: 0.8056 (m-80) cc_final: 0.7828 (m-80) REVERT: B 291 LEU cc_start: 0.9643 (mt) cc_final: 0.9358 (mt) REVERT: B 314 MET cc_start: 0.8759 (ttp) cc_final: 0.8243 (ttp) REVERT: B 317 MET cc_start: 0.8720 (mtt) cc_final: 0.8216 (mpp) REVERT: B 335 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 375 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7971 (mmmm) REVERT: B 377 LYS cc_start: 0.7765 (mttt) cc_final: 0.7427 (mttp) REVERT: B 403 ILE cc_start: 0.9260 (mm) cc_final: 0.9021 (mm) REVERT: B 415 ASN cc_start: 0.9051 (t0) cc_final: 0.8747 (t0) REVERT: B 447 ASN cc_start: 0.8565 (m-40) cc_final: 0.8317 (m110) REVERT: B 475 ASN cc_start: 0.8989 (m-40) cc_final: 0.8746 (m-40) REVERT: B 496 ASN cc_start: 0.9491 (t0) cc_final: 0.9155 (t0) REVERT: B 501 GLN cc_start: 0.9520 (tt0) cc_final: 0.9210 (tt0) REVERT: B 571 TYR cc_start: 0.8878 (t80) cc_final: 0.8502 (t80) REVERT: B 588 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8883 (mm-40) REVERT: B 636 LYS cc_start: 0.9460 (mmpt) cc_final: 0.9173 (mmmt) REVERT: B 640 MET cc_start: 0.9139 (tpp) cc_final: 0.8927 (tpp) REVERT: B 645 GLN cc_start: 0.9195 (tp40) cc_final: 0.8863 (tp-100) REVERT: C 130 TYR cc_start: 0.8953 (m-80) cc_final: 0.8593 (m-80) REVERT: C 157 MET cc_start: 0.8388 (mtm) cc_final: 0.7811 (mtm) REVERT: D 82 ASP cc_start: 0.9016 (m-30) cc_final: 0.8465 (p0) REVERT: D 116 GLU cc_start: 0.9466 (pm20) cc_final: 0.9054 (tm-30) REVERT: D 137 MET cc_start: 0.6522 (ttt) cc_final: 0.6096 (tmm) REVERT: D 185 MET cc_start: 0.4286 (mmp) cc_final: 0.3883 (mpp) REVERT: D 235 LEU cc_start: 0.7740 (mp) cc_final: 0.7250 (mt) REVERT: D 242 TYR cc_start: 0.9105 (t80) cc_final: 0.8801 (t80) REVERT: D 262 TYR cc_start: 0.8804 (t80) cc_final: 0.8514 (t80) REVERT: E 25 TRP cc_start: 0.8448 (p-90) cc_final: 0.7683 (p-90) REVERT: E 34 MET cc_start: 0.9009 (mpp) cc_final: 0.8769 (ptp) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.1183 time to fit residues: 109.3859 Evaluate side-chains 514 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 25 GLN A 191 GLN A 475 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103606 restraints weight = 44843.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.107568 restraints weight = 27387.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110268 restraints weight = 18784.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112013 restraints weight = 14031.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113223 restraints weight = 11226.028| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17041 Z= 0.136 Angle : 0.612 9.145 23026 Z= 0.322 Chirality : 0.043 0.185 2464 Planarity : 0.004 0.055 2931 Dihedral : 8.867 134.805 2373 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2012 helix: 1.02 (0.15), residues: 1175 sheet: -0.51 (0.37), residues: 187 loop : 0.15 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.023 0.002 TYR A 471 PHE 0.028 0.002 PHE C 227 TRP 0.007 0.001 TRP B 558 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (17038) covalent geometry : angle 0.60748 / 0.32 (23020) SS BOND : bond 0.00754 / 0.36 ( 3) SS BOND : angle 4.38955 / 2.10 ( 6) hydrogen bonds : bond 0.04172 / 2.70 ( 912) hydrogen bonds : angle 5.04406 / 3.50 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.9227 (m-40) cc_final: 0.8915 (m110) REVERT: A 147 GLN cc_start: 0.9242 (mt0) cc_final: 0.8758 (mt0) REVERT: A 186 ILE cc_start: 0.9547 (mm) cc_final: 0.9174 (mm) REVERT: A 188 ILE cc_start: 0.9548 (mt) cc_final: 0.9195 (mt) REVERT: A 190 MET cc_start: 0.9254 (mtm) cc_final: 0.8983 (mtm) REVERT: A 202 ASN cc_start: 0.8646 (t0) cc_final: 0.8359 (t0) REVERT: A 223 VAL cc_start: 0.9115 (p) cc_final: 0.8894 (p) REVERT: A 250 TYR cc_start: 0.7295 (m-80) cc_final: 0.6986 (m-80) REVERT: A 255 HIS cc_start: 0.8213 (t-90) cc_final: 0.7810 (t70) REVERT: A 257 ASP cc_start: 0.8645 (m-30) cc_final: 0.8123 (m-30) REVERT: A 263 ASP cc_start: 0.9021 (m-30) cc_final: 0.8682 (m-30) REVERT: A 291 LEU cc_start: 0.9675 (mp) cc_final: 0.9296 (mp) REVERT: A 301 PHE cc_start: 0.8877 (m-80) cc_final: 0.8316 (m-80) REVERT: A 312 GLN cc_start: 0.8452 (tp40) cc_final: 0.8036 (tp40) REVERT: A 317 MET cc_start: 0.9114 (mmm) cc_final: 0.8816 (mmm) REVERT: A 320 ASN cc_start: 0.8634 (m-40) cc_final: 0.8280 (m110) REVERT: A 322 MET cc_start: 0.8860 (mmm) cc_final: 0.8483 (mmm) REVERT: A 366 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8937 (ptpt) REVERT: A 375 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8437 (mmtm) REVERT: A 378 PHE cc_start: 0.7912 (p90) cc_final: 0.7686 (p90) REVERT: A 393 SER cc_start: 0.9095 (t) cc_final: 0.8358 (t) REVERT: A 402 GLU cc_start: 0.8157 (mp0) cc_final: 0.7527 (mp0) REVERT: A 494 MET cc_start: 0.8521 (mmt) cc_final: 0.8082 (mmt) REVERT: A 501 GLN cc_start: 0.9419 (tt0) cc_final: 0.8942 (tm-30) REVERT: A 510 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8571 (tptp) REVERT: A 571 TYR cc_start: 0.8780 (t80) cc_final: 0.7947 (t80) REVERT: A 590 SER cc_start: 0.9106 (t) cc_final: 0.8214 (p) REVERT: A 615 MET cc_start: 0.8975 (mmp) cc_final: 0.8660 (mmp) REVERT: A 664 THR cc_start: 0.9444 (p) cc_final: 0.9003 (p) REVERT: A 667 LEU cc_start: 0.9307 (tt) cc_final: 0.9104 (tt) REVERT: A 668 ASN cc_start: 0.9017 (m-40) cc_final: 0.8758 (m-40) REVERT: A 686 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7315 (mmm160) REVERT: B 10 ILE cc_start: 0.9699 (mt) cc_final: 0.9398 (tp) REVERT: B 40 TYR cc_start: 0.9225 (t80) cc_final: 0.8951 (t80) REVERT: B 95 MET cc_start: 0.8820 (tpp) cc_final: 0.8550 (tpp) REVERT: B 99 LYS cc_start: 0.9436 (tptp) cc_final: 0.9027 (tptp) REVERT: B 147 GLN cc_start: 0.8385 (mp10) cc_final: 0.8130 (mp10) REVERT: B 167 LEU cc_start: 0.8994 (mt) cc_final: 0.8738 (mt) REVERT: B 172 LEU cc_start: 0.8862 (mp) cc_final: 0.8655 (mp) REVERT: B 184 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8430 (ttm-80) REVERT: B 186 ILE cc_start: 0.9746 (mt) cc_final: 0.9449 (mt) REVERT: B 190 MET cc_start: 0.9398 (mtm) cc_final: 0.9071 (mtm) REVERT: B 191 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8878 (mm-40) REVERT: B 250 TYR cc_start: 0.7929 (m-80) cc_final: 0.7588 (m-80) REVERT: B 317 MET cc_start: 0.8613 (mtt) cc_final: 0.8266 (mpp) REVERT: B 335 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 348 MET cc_start: 0.8421 (tpt) cc_final: 0.8219 (tpp) REVERT: B 375 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8052 (mmmm) REVERT: B 403 ILE cc_start: 0.9180 (mm) cc_final: 0.8918 (mm) REVERT: B 430 LYS cc_start: 0.9108 (mttt) cc_final: 0.8896 (mmtt) REVERT: B 447 ASN cc_start: 0.8587 (m-40) cc_final: 0.7999 (m110) REVERT: B 493 MET cc_start: 0.9237 (tmm) cc_final: 0.8919 (tmm) REVERT: B 501 GLN cc_start: 0.9554 (tt0) cc_final: 0.9287 (tt0) REVERT: B 570 MET cc_start: 0.8569 (tpp) cc_final: 0.8274 (tpp) REVERT: B 571 TYR cc_start: 0.8755 (t80) cc_final: 0.8374 (t80) REVERT: B 575 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7727 (ptp-170) REVERT: B 588 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8794 (mm-40) REVERT: B 645 GLN cc_start: 0.9203 (tp40) cc_final: 0.8755 (tp40) REVERT: B 652 ILE cc_start: 0.9203 (mt) cc_final: 0.8961 (mt) REVERT: C 130 TYR cc_start: 0.9002 (m-80) cc_final: 0.8793 (m-80) REVERT: C 157 MET cc_start: 0.8295 (mtm) cc_final: 0.7843 (mtm) REVERT: C 200 ILE cc_start: 0.8536 (pt) cc_final: 0.8320 (pt) REVERT: C 237 GLU cc_start: 0.9615 (mp0) cc_final: 0.9405 (pp20) REVERT: C 276 TYR cc_start: 0.8311 (t80) cc_final: 0.8091 (t80) REVERT: D 82 ASP cc_start: 0.8993 (m-30) cc_final: 0.8441 (p0) REVERT: D 117 THR cc_start: 0.9374 (p) cc_final: 0.8871 (p) REVERT: D 137 MET cc_start: 0.6721 (ttt) cc_final: 0.6382 (tmm) REVERT: D 242 TYR cc_start: 0.9119 (t80) cc_final: 0.8881 (t80) REVERT: D 262 TYR cc_start: 0.8691 (t80) cc_final: 0.8434 (t80) REVERT: E 25 TRP cc_start: 0.8370 (p-90) cc_final: 0.7568 (p-90) outliers start: 1 outliers final: 1 residues processed: 632 average time/residue: 0.1225 time to fit residues: 117.5151 Evaluate side-chains 516 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 515 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 104 optimal weight: 0.0010 chunk 172 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.147990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103695 restraints weight = 45909.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107450 restraints weight = 28217.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110057 restraints weight = 19301.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111784 restraints weight = 14383.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112934 restraints weight = 11477.823| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17041 Z= 0.170 Angle : 0.628 9.297 23026 Z= 0.330 Chirality : 0.043 0.185 2464 Planarity : 0.004 0.051 2931 Dihedral : 8.692 135.410 2373 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2012 helix: 1.03 (0.15), residues: 1174 sheet: -0.39 (0.38), residues: 185 loop : -0.01 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 164 TYR 0.018 0.002 TYR D 105 PHE 0.024 0.002 PHE D 320 TRP 0.007 0.001 TRP B 558 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (17038) covalent geometry : angle 0.62479 / 0.33 (23020) SS BOND : bond 0.00699 / 0.36 ( 3) SS BOND : angle 3.71850 / 1.82 ( 6) hydrogen bonds : bond 0.04151 / 2.67 ( 912) hydrogen bonds : angle 5.02120 / 3.47 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9224 (tp) cc_final: 0.8915 (tp) REVERT: A 54 LYS cc_start: 0.9682 (tttt) cc_final: 0.8750 (ttpt) REVERT: A 89 PHE cc_start: 0.9472 (t80) cc_final: 0.9183 (t80) REVERT: A 117 ARG cc_start: 0.9010 (mtt-85) cc_final: 0.8619 (mtt90) REVERT: A 142 ASN cc_start: 0.9212 (m-40) cc_final: 0.8926 (m110) REVERT: A 186 ILE cc_start: 0.9551 (mm) cc_final: 0.9219 (mm) REVERT: A 188 ILE cc_start: 0.9545 (mt) cc_final: 0.9312 (mt) REVERT: A 190 MET cc_start: 0.9295 (mtm) cc_final: 0.9015 (mtm) REVERT: A 202 ASN cc_start: 0.8763 (t0) cc_final: 0.8476 (t0) REVERT: A 250 TYR cc_start: 0.7281 (m-80) cc_final: 0.6836 (m-80) REVERT: A 255 HIS cc_start: 0.8225 (t-90) cc_final: 0.7511 (t70) REVERT: A 257 ASP cc_start: 0.8706 (m-30) cc_final: 0.8263 (m-30) REVERT: A 263 ASP cc_start: 0.9032 (m-30) cc_final: 0.8714 (m-30) REVERT: A 290 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9008 (tm-30) REVERT: A 291 LEU cc_start: 0.9660 (mp) cc_final: 0.9182 (mt) REVERT: A 301 PHE cc_start: 0.8827 (m-80) cc_final: 0.8365 (m-80) REVERT: A 322 MET cc_start: 0.8792 (mmm) cc_final: 0.8542 (mmm) REVERT: A 366 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8917 (ptpt) REVERT: A 378 PHE cc_start: 0.8183 (p90) cc_final: 0.7844 (p90) REVERT: A 393 SER cc_start: 0.9192 (t) cc_final: 0.8308 (t) REVERT: A 402 GLU cc_start: 0.8195 (mp0) cc_final: 0.7567 (mp0) REVERT: A 447 ASN cc_start: 0.8919 (m-40) cc_final: 0.8585 (m-40) REVERT: A 474 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8790 (mm-40) REVERT: A 501 GLN cc_start: 0.9425 (tt0) cc_final: 0.9101 (tm-30) REVERT: A 571 TYR cc_start: 0.8831 (t80) cc_final: 0.8212 (t80) REVERT: A 588 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8246 (mm-40) REVERT: A 601 ILE cc_start: 0.9463 (tt) cc_final: 0.9092 (tt) REVERT: A 615 MET cc_start: 0.9026 (mmp) cc_final: 0.8664 (mmp) REVERT: A 658 LEU cc_start: 0.8896 (mm) cc_final: 0.8390 (mm) REVERT: A 664 THR cc_start: 0.9417 (p) cc_final: 0.9005 (p) REVERT: A 668 ASN cc_start: 0.9240 (m-40) cc_final: 0.8913 (m-40) REVERT: A 686 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7752 (mmm160) REVERT: B 40 TYR cc_start: 0.9228 (t80) cc_final: 0.8918 (t80) REVERT: B 95 MET cc_start: 0.8900 (tpp) cc_final: 0.8564 (tpp) REVERT: B 99 LYS cc_start: 0.9444 (tptp) cc_final: 0.9006 (tptp) REVERT: B 147 GLN cc_start: 0.8489 (mp10) cc_final: 0.8084 (mp10) REVERT: B 150 GLN cc_start: 0.9125 (tp40) cc_final: 0.8831 (tp40) REVERT: B 167 LEU cc_start: 0.9018 (mt) cc_final: 0.8723 (mt) REVERT: B 186 ILE cc_start: 0.9658 (mt) cc_final: 0.9422 (mt) REVERT: B 190 MET cc_start: 0.9419 (mtm) cc_final: 0.9098 (mtm) REVERT: B 205 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7889 (mmmm) REVERT: B 227 MET cc_start: 0.9219 (ptp) cc_final: 0.8612 (ptp) REVERT: B 235 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7921 (mtm-85) REVERT: B 250 TYR cc_start: 0.8069 (m-80) cc_final: 0.7792 (m-80) REVERT: B 314 MET cc_start: 0.8842 (ttp) cc_final: 0.8037 (ttp) REVERT: B 317 MET cc_start: 0.8480 (mtt) cc_final: 0.8130 (mpp) REVERT: B 335 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 370 ASN cc_start: 0.9522 (m110) cc_final: 0.9236 (m110) REVERT: B 375 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8022 (mmmm) REVERT: B 403 ILE cc_start: 0.9114 (mm) cc_final: 0.8817 (mm) REVERT: B 471 TYR cc_start: 0.9299 (t80) cc_final: 0.8956 (t80) REVERT: B 475 ASN cc_start: 0.9150 (m-40) cc_final: 0.8738 (m-40) REVERT: B 496 ASN cc_start: 0.9513 (t0) cc_final: 0.9228 (t0) REVERT: B 500 ILE cc_start: 0.9710 (mt) cc_final: 0.9503 (mt) REVERT: B 501 GLN cc_start: 0.9576 (tt0) cc_final: 0.9329 (tm-30) REVERT: B 570 MET cc_start: 0.8652 (tpp) cc_final: 0.8449 (tpp) REVERT: B 571 TYR cc_start: 0.8891 (t80) cc_final: 0.8615 (t80) REVERT: B 575 ARG cc_start: 0.8117 (ptp-170) cc_final: 0.7758 (ptp-170) REVERT: B 588 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8738 (mm-40) REVERT: B 645 GLN cc_start: 0.9250 (tp40) cc_final: 0.8823 (tp40) REVERT: B 650 GLN cc_start: 0.7010 (mt0) cc_final: 0.6128 (mt0) REVERT: B 652 ILE cc_start: 0.9267 (mt) cc_final: 0.9039 (mt) REVERT: C 95 MET cc_start: -0.2251 (ptm) cc_final: -0.2503 (ptm) REVERT: C 157 MET cc_start: 0.8325 (mtm) cc_final: 0.7944 (mtm) REVERT: C 197 ASP cc_start: 0.8292 (m-30) cc_final: 0.7055 (m-30) REVERT: C 200 ILE cc_start: 0.8460 (pt) cc_final: 0.8121 (pt) REVERT: C 201 HIS cc_start: 0.7266 (m170) cc_final: 0.7037 (t-170) REVERT: C 212 ILE cc_start: 0.6592 (mt) cc_final: 0.6269 (mt) REVERT: D 74 MET cc_start: 0.7071 (tpp) cc_final: 0.6308 (ptt) REVERT: D 82 ASP cc_start: 0.9004 (m-30) cc_final: 0.8447 (p0) REVERT: D 242 TYR cc_start: 0.9133 (t80) cc_final: 0.8795 (t80) REVERT: D 262 TYR cc_start: 0.8885 (t80) cc_final: 0.8634 (t80) REVERT: E 25 TRP cc_start: 0.8428 (p-90) cc_final: 0.7091 (p-90) REVERT: E 93 LYS cc_start: 0.6513 (mmtm) cc_final: 0.6194 (mmmt) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1277 time to fit residues: 116.6565 Evaluate side-chains 500 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 195 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 312 GLN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 107 ASN D 132 GLN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.151906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106523 restraints weight = 45146.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110414 restraints weight = 27610.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113105 restraints weight = 18887.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114865 restraints weight = 14146.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116004 restraints weight = 11359.750| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17041 Z= 0.133 Angle : 0.619 8.497 23026 Z= 0.324 Chirality : 0.043 0.185 2464 Planarity : 0.004 0.070 2931 Dihedral : 8.266 132.159 2373 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2012 helix: 1.02 (0.15), residues: 1173 sheet: -0.46 (0.38), residues: 193 loop : -0.10 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 164 TYR 0.023 0.001 TYR B 118 PHE 0.023 0.002 PHE C 227 TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (17038) covalent geometry : angle 0.61549 / 0.32 (23020) SS BOND : bond 0.00453 / 0.23 ( 3) SS BOND : angle 3.99624 / 1.92 ( 6) hydrogen bonds : bond 0.03958 / 2.56 ( 912) hydrogen bonds : angle 4.98216 / 3.48 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9064 (tp) cc_final: 0.8845 (tp) REVERT: A 89 PHE cc_start: 0.9393 (t80) cc_final: 0.9164 (t80) REVERT: A 157 LEU cc_start: 0.9234 (tp) cc_final: 0.9024 (tp) REVERT: A 164 ARG cc_start: 0.8454 (ttp80) cc_final: 0.7697 (ttp80) REVERT: A 186 ILE cc_start: 0.9563 (mm) cc_final: 0.9277 (mm) REVERT: A 188 ILE cc_start: 0.9518 (mt) cc_final: 0.9162 (mt) REVERT: A 190 MET cc_start: 0.9279 (mtm) cc_final: 0.9067 (mtm) REVERT: A 191 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8609 (mt0) REVERT: A 250 TYR cc_start: 0.7090 (m-80) cc_final: 0.6731 (m-80) REVERT: A 255 HIS cc_start: 0.8259 (t-90) cc_final: 0.7574 (t70) REVERT: A 257 ASP cc_start: 0.8684 (m-30) cc_final: 0.8282 (m-30) REVERT: A 290 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8938 (tm-30) REVERT: A 291 LEU cc_start: 0.9626 (mp) cc_final: 0.9046 (mt) REVERT: A 301 PHE cc_start: 0.8684 (m-80) cc_final: 0.8389 (m-80) REVERT: A 322 MET cc_start: 0.8823 (mmm) cc_final: 0.8582 (mmm) REVERT: A 366 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8901 (ptpt) REVERT: A 375 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8452 (mmtm) REVERT: A 378 PHE cc_start: 0.8118 (p90) cc_final: 0.7782 (p90) REVERT: A 390 GLN cc_start: 0.8568 (mm110) cc_final: 0.8342 (mm-40) REVERT: A 393 SER cc_start: 0.9162 (t) cc_final: 0.8222 (t) REVERT: A 402 GLU cc_start: 0.8291 (mp0) cc_final: 0.7556 (mp0) REVERT: A 403 ILE cc_start: 0.8503 (mm) cc_final: 0.8278 (mm) REVERT: A 447 ASN cc_start: 0.8900 (m-40) cc_final: 0.8349 (m-40) REVERT: A 456 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8990 (mtmm) REVERT: A 493 MET cc_start: 0.8544 (ttt) cc_final: 0.7913 (ttp) REVERT: A 494 MET cc_start: 0.8349 (mmt) cc_final: 0.7864 (mmt) REVERT: A 501 GLN cc_start: 0.9416 (tt0) cc_final: 0.9070 (tm-30) REVERT: A 586 TYR cc_start: 0.9140 (m-80) cc_final: 0.8430 (m-80) REVERT: A 615 MET cc_start: 0.9111 (mmp) cc_final: 0.8792 (mmp) REVERT: A 658 LEU cc_start: 0.8355 (mm) cc_final: 0.8145 (mm) REVERT: A 664 THR cc_start: 0.9251 (p) cc_final: 0.8911 (p) REVERT: A 667 LEU cc_start: 0.9514 (tt) cc_final: 0.9287 (tt) REVERT: A 686 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7768 (mmm160) REVERT: B 10 ILE cc_start: 0.9717 (mt) cc_final: 0.9402 (tp) REVERT: B 40 TYR cc_start: 0.9151 (t80) cc_final: 0.8854 (t80) REVERT: B 95 MET cc_start: 0.8860 (tpp) cc_final: 0.8421 (tpp) REVERT: B 99 LYS cc_start: 0.9448 (tptp) cc_final: 0.9132 (tptp) REVERT: B 128 PHE cc_start: 0.9635 (t80) cc_final: 0.9434 (t80) REVERT: B 129 PHE cc_start: 0.9451 (m-10) cc_final: 0.8916 (m-80) REVERT: B 139 GLU cc_start: 0.9182 (mp0) cc_final: 0.8923 (mp0) REVERT: B 147 GLN cc_start: 0.8583 (mp10) cc_final: 0.8176 (mp10) REVERT: B 150 GLN cc_start: 0.9241 (tp40) cc_final: 0.8901 (tp-100) REVERT: B 167 LEU cc_start: 0.8944 (mt) cc_final: 0.8457 (mt) REVERT: B 174 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7764 (tp30) REVERT: B 184 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8822 (ttp-170) REVERT: B 227 MET cc_start: 0.9171 (ptp) cc_final: 0.8644 (ptp) REVERT: B 250 TYR cc_start: 0.8051 (m-80) cc_final: 0.7814 (m-80) REVERT: B 274 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8354 (mmm160) REVERT: B 314 MET cc_start: 0.8744 (ttp) cc_final: 0.7899 (ttp) REVERT: B 317 MET cc_start: 0.8311 (mtt) cc_final: 0.8066 (mpp) REVERT: B 335 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 370 ASN cc_start: 0.9320 (m110) cc_final: 0.8806 (m110) REVERT: B 391 VAL cc_start: 0.8963 (p) cc_final: 0.7916 (p) REVERT: B 399 GLU cc_start: 0.8937 (tp30) cc_final: 0.8417 (tp30) REVERT: B 403 ILE cc_start: 0.9082 (mm) cc_final: 0.8824 (mm) REVERT: B 456 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8603 (mmtm) REVERT: B 475 ASN cc_start: 0.9180 (m-40) cc_final: 0.8842 (p0) REVERT: B 501 GLN cc_start: 0.9590 (tt0) cc_final: 0.9293 (tm-30) REVERT: B 570 MET cc_start: 0.8539 (tpp) cc_final: 0.8212 (tpp) REVERT: B 571 TYR cc_start: 0.8814 (t80) cc_final: 0.8568 (t80) REVERT: B 575 ARG cc_start: 0.7940 (ptp-170) cc_final: 0.7512 (ptp-170) REVERT: B 640 MET cc_start: 0.9040 (tpp) cc_final: 0.8773 (tpp) REVERT: B 645 GLN cc_start: 0.9246 (tp40) cc_final: 0.8835 (tp40) REVERT: B 652 ILE cc_start: 0.9251 (mt) cc_final: 0.9034 (mt) REVERT: C 157 MET cc_start: 0.8135 (mtm) cc_final: 0.7725 (mtm) REVERT: C 197 ASP cc_start: 0.8038 (m-30) cc_final: 0.6839 (m-30) REVERT: C 200 ILE cc_start: 0.8326 (pt) cc_final: 0.7893 (pt) REVERT: C 201 HIS cc_start: 0.7421 (m170) cc_final: 0.6874 (t70) REVERT: C 212 ILE cc_start: 0.6380 (mt) cc_final: 0.5969 (mt) REVERT: C 276 TYR cc_start: 0.8638 (t80) cc_final: 0.8338 (t80) REVERT: D 20 MET cc_start: 0.9229 (tpp) cc_final: 0.9020 (tpp) REVERT: D 74 MET cc_start: 0.7322 (tpp) cc_final: 0.6721 (ptt) REVERT: D 82 ASP cc_start: 0.8977 (m-30) cc_final: 0.8471 (p0) REVERT: D 185 MET cc_start: 0.4330 (mmm) cc_final: 0.3447 (mmm) REVERT: D 242 TYR cc_start: 0.9119 (t80) cc_final: 0.8803 (t80) REVERT: D 262 TYR cc_start: 0.8880 (t80) cc_final: 0.8637 (t80) REVERT: E 25 TRP cc_start: 0.8403 (p-90) cc_final: 0.7070 (p-90) REVERT: E 93 LYS cc_start: 0.6565 (mmtm) cc_final: 0.6322 (mmmt) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.1280 time to fit residues: 117.0732 Evaluate side-chains 496 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 7.9990 chunk 64 optimal weight: 0.0020 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 175 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.5128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 320 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 107 ASN D 28 GLN D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.154224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108176 restraints weight = 44796.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112295 restraints weight = 27020.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115079 restraints weight = 18337.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116899 restraints weight = 13650.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118103 restraints weight = 10878.663| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17041 Z= 0.128 Angle : 0.628 8.708 23026 Z= 0.329 Chirality : 0.044 0.195 2464 Planarity : 0.003 0.039 2931 Dihedral : 8.012 137.906 2373 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2012 helix: 1.04 (0.15), residues: 1177 sheet: -0.19 (0.41), residues: 169 loop : -0.12 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.016 0.001 TYR B 36 PHE 0.031 0.002 PHE A 654 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (17038) covalent geometry : angle 0.62477 / 0.33 (23020) SS BOND : bond 0.00611 / 0.30 ( 3) SS BOND : angle 4.13079 / 2.01 ( 6) hydrogen bonds : bond 0.03906 / 2.52 ( 912) hydrogen bonds : angle 4.94898 / 3.46 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8126 (ttp80) REVERT: A 186 ILE cc_start: 0.9585 (mm) cc_final: 0.9318 (mm) REVERT: A 188 ILE cc_start: 0.9540 (mt) cc_final: 0.9194 (mt) REVERT: A 250 TYR cc_start: 0.7211 (m-80) cc_final: 0.6800 (m-80) REVERT: A 255 HIS cc_start: 0.8293 (t-90) cc_final: 0.7644 (t70) REVERT: A 257 ASP cc_start: 0.8636 (m-30) cc_final: 0.8250 (m-30) REVERT: A 290 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8909 (tm-30) REVERT: A 291 LEU cc_start: 0.9608 (mp) cc_final: 0.9028 (mt) REVERT: A 301 PHE cc_start: 0.8559 (m-80) cc_final: 0.8305 (m-80) REVERT: A 366 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8880 (ptpp) REVERT: A 375 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8402 (mmtm) REVERT: A 393 SER cc_start: 0.9082 (t) cc_final: 0.8254 (t) REVERT: A 402 GLU cc_start: 0.8320 (mp0) cc_final: 0.7638 (mp0) REVERT: A 447 ASN cc_start: 0.8902 (m-40) cc_final: 0.8346 (m-40) REVERT: A 456 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8954 (mtmm) REVERT: A 474 GLN cc_start: 0.8927 (mm110) cc_final: 0.8370 (mp10) REVERT: A 493 MET cc_start: 0.8530 (ttt) cc_final: 0.7841 (ttp) REVERT: A 494 MET cc_start: 0.8353 (mmt) cc_final: 0.7807 (mmt) REVERT: A 501 GLN cc_start: 0.9412 (tt0) cc_final: 0.9004 (tm-30) REVERT: A 510 LYS cc_start: 0.8920 (tmtt) cc_final: 0.8400 (tptp) REVERT: A 586 TYR cc_start: 0.9135 (m-80) cc_final: 0.8580 (m-80) REVERT: A 686 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7777 (mmm160) REVERT: B 10 ILE cc_start: 0.9710 (mt) cc_final: 0.9376 (tp) REVERT: B 40 TYR cc_start: 0.9116 (t80) cc_final: 0.8801 (t80) REVERT: B 95 MET cc_start: 0.8761 (tpp) cc_final: 0.8420 (tpp) REVERT: B 99 LYS cc_start: 0.9457 (tptp) cc_final: 0.9197 (tptp) REVERT: B 129 PHE cc_start: 0.9463 (m-10) cc_final: 0.8978 (m-80) REVERT: B 167 LEU cc_start: 0.8853 (mt) cc_final: 0.8505 (mt) REVERT: B 174 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7719 (tp30) REVERT: B 184 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8817 (ttp-170) REVERT: B 227 MET cc_start: 0.9203 (ptp) cc_final: 0.8633 (ptp) REVERT: B 235 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: B 274 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8363 (mmm160) REVERT: B 350 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8318 (mmm160) REVERT: B 375 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8336 (mtpt) REVERT: B 390 GLN cc_start: 0.9281 (mt0) cc_final: 0.9052 (mm-40) REVERT: B 403 ILE cc_start: 0.9018 (mm) cc_final: 0.8780 (mm) REVERT: B 445 ILE cc_start: 0.8957 (mm) cc_final: 0.8532 (mm) REVERT: B 456 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8678 (mmtm) REVERT: B 475 ASN cc_start: 0.9205 (m-40) cc_final: 0.8963 (m110) REVERT: B 483 GLU cc_start: 0.9293 (pm20) cc_final: 0.8993 (pm20) REVERT: B 496 ASN cc_start: 0.9462 (t0) cc_final: 0.9109 (t0) REVERT: B 500 ILE cc_start: 0.9711 (mt) cc_final: 0.9502 (mt) REVERT: B 501 GLN cc_start: 0.9513 (tt0) cc_final: 0.9234 (tm-30) REVERT: B 570 MET cc_start: 0.8457 (tpp) cc_final: 0.8160 (tpp) REVERT: B 571 TYR cc_start: 0.8749 (t80) cc_final: 0.8460 (t80) REVERT: B 575 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.7326 (ptp-170) REVERT: B 598 MET cc_start: 0.8519 (ttm) cc_final: 0.8235 (ttm) REVERT: B 602 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 604 ARG cc_start: 0.9402 (mmp80) cc_final: 0.9036 (mmp80) REVERT: B 645 GLN cc_start: 0.9242 (tp40) cc_final: 0.8811 (tp40) REVERT: B 652 ILE cc_start: 0.9178 (mt) cc_final: 0.8962 (mt) REVERT: B 656 LEU cc_start: 0.8882 (mm) cc_final: 0.8647 (mm) REVERT: C 200 ILE cc_start: 0.8439 (pt) cc_final: 0.8144 (pt) REVERT: C 276 TYR cc_start: 0.8611 (t80) cc_final: 0.8285 (t80) REVERT: C 315 LEU cc_start: 0.8098 (mt) cc_final: 0.7896 (mt) REVERT: D 74 MET cc_start: 0.7574 (tpp) cc_final: 0.6823 (ptt) REVERT: D 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.8743 (p0) REVERT: D 242 TYR cc_start: 0.9068 (t80) cc_final: 0.8798 (t80) REVERT: D 262 TYR cc_start: 0.8865 (t80) cc_final: 0.8633 (t80) REVERT: E 25 TRP cc_start: 0.8318 (p-90) cc_final: 0.7012 (p-90) REVERT: E 93 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6351 (mmmt) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.1263 time to fit residues: 113.7787 Evaluate side-chains 500 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 188 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 390 GLN B 11 GLN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** 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 = 0.4059 r_free = 0.4059 target = 0.151914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106272 restraints weight = 45695.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110419 restraints weight = 26955.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113110 restraints weight = 18246.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114770 restraints weight = 13582.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116067 restraints weight = 10862.627| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17041 Z= 0.149 Angle : 0.662 16.294 23026 Z= 0.347 Chirality : 0.045 0.208 2464 Planarity : 0.004 0.047 2931 Dihedral : 7.974 140.472 2373 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 2012 helix: 0.91 (0.15), residues: 1180 sheet: -0.29 (0.41), residues: 169 loop : -0.16 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 161 TYR 0.023 0.001 TYR D 174 PHE 0.043 0.002 PHE C 109 TRP 0.009 0.001 TRP D 30 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (17038) covalent geometry : angle 0.65694 / 0.34 (23020) SS BOND : bond 0.00490 / 0.25 ( 3) SS BOND : angle 5.32487 / 2.51 ( 6) hydrogen bonds : bond 0.04014 / 2.58 ( 912) hydrogen bonds : angle 5.02883 / 3.55 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.9048 (mp0) cc_final: 0.8840 (mp0) REVERT: A 164 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8158 (ttp80) REVERT: A 188 ILE cc_start: 0.9526 (mt) cc_final: 0.9181 (mt) REVERT: A 190 MET cc_start: 0.9358 (mtm) cc_final: 0.8986 (mtm) REVERT: A 191 GLN cc_start: 0.8096 (mt0) cc_final: 0.7826 (mt0) REVERT: A 250 TYR cc_start: 0.7257 (m-80) cc_final: 0.6847 (m-80) REVERT: A 255 HIS cc_start: 0.8344 (t-90) cc_final: 0.7756 (t70) REVERT: A 257 ASP cc_start: 0.8791 (m-30) cc_final: 0.8360 (m-30) REVERT: A 290 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8902 (tm-30) REVERT: A 291 LEU cc_start: 0.9620 (mp) cc_final: 0.9024 (mt) REVERT: A 301 PHE cc_start: 0.8769 (m-80) cc_final: 0.8427 (m-80) REVERT: A 317 MET cc_start: 0.9075 (mmt) cc_final: 0.8868 (mmt) REVERT: A 322 MET cc_start: 0.8937 (mmm) cc_final: 0.8729 (mmm) REVERT: A 366 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8873 (ptpp) REVERT: A 447 ASN cc_start: 0.8934 (m-40) cc_final: 0.8733 (m-40) REVERT: A 456 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8941 (mtmm) REVERT: A 474 GLN cc_start: 0.8911 (mm110) cc_final: 0.8470 (mp10) REVERT: A 493 MET cc_start: 0.8537 (ttt) cc_final: 0.7822 (ttp) REVERT: A 494 MET cc_start: 0.8335 (mmt) cc_final: 0.7748 (mmt) REVERT: A 501 GLN cc_start: 0.9426 (tt0) cc_final: 0.8984 (tm-30) REVERT: A 510 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8512 (tptp) REVERT: A 586 TYR cc_start: 0.9129 (m-80) cc_final: 0.8645 (m-80) REVERT: A 615 MET cc_start: 0.9013 (mmp) cc_final: 0.8493 (mmp) REVERT: A 667 LEU cc_start: 0.9662 (tt) cc_final: 0.9425 (tt) REVERT: A 686 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7819 (mmm160) REVERT: B 10 ILE cc_start: 0.9719 (mt) cc_final: 0.9387 (tp) REVERT: B 40 TYR cc_start: 0.9098 (t80) cc_final: 0.8768 (t80) REVERT: B 95 MET cc_start: 0.8765 (tpp) cc_final: 0.8444 (tpp) REVERT: B 99 LYS cc_start: 0.9463 (tptp) cc_final: 0.9215 (tptp) REVERT: B 129 PHE cc_start: 0.9440 (m-10) cc_final: 0.8907 (m-80) REVERT: B 150 GLN cc_start: 0.9225 (tp40) cc_final: 0.8942 (tp40) REVERT: B 167 LEU cc_start: 0.8924 (mt) cc_final: 0.8596 (mt) REVERT: B 174 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7699 (tp30) REVERT: B 184 ARG cc_start: 0.9043 (ttm-80) cc_final: 0.8801 (ttp-170) REVERT: B 187 ASP cc_start: 0.8672 (t0) cc_final: 0.8087 (t0) REVERT: B 227 MET cc_start: 0.9157 (ptp) cc_final: 0.8625 (ptp) REVERT: B 274 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8373 (mmm160) REVERT: B 308 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8831 (ptpp) REVERT: B 314 MET cc_start: 0.8827 (ttp) cc_final: 0.8252 (tmm) REVERT: B 350 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8427 (mmm160) REVERT: B 375 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8385 (mtpt) REVERT: B 390 GLN cc_start: 0.9259 (mt0) cc_final: 0.9047 (mm-40) REVERT: B 399 GLU cc_start: 0.8900 (tp30) cc_final: 0.8368 (tp30) REVERT: B 400 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8775 (mm-30) REVERT: B 403 ILE cc_start: 0.9049 (mm) cc_final: 0.8779 (mm) REVERT: B 415 ASN cc_start: 0.8950 (t0) cc_final: 0.8648 (t0) REVERT: B 494 MET cc_start: 0.9029 (ttm) cc_final: 0.8819 (mmt) REVERT: B 496 ASN cc_start: 0.9453 (t0) cc_final: 0.9113 (t0) REVERT: B 500 ILE cc_start: 0.9710 (mt) cc_final: 0.9497 (mt) REVERT: B 570 MET cc_start: 0.8536 (tpp) cc_final: 0.8217 (tpp) REVERT: B 571 TYR cc_start: 0.8794 (t80) cc_final: 0.8532 (t80) REVERT: B 575 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7441 (ptp-170) REVERT: B 598 MET cc_start: 0.8451 (ttm) cc_final: 0.8171 (ttm) REVERT: B 602 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 604 ARG cc_start: 0.9406 (mmp80) cc_final: 0.9103 (mmp80) REVERT: B 645 GLN cc_start: 0.9236 (tp40) cc_final: 0.8823 (tp40) REVERT: B 652 ILE cc_start: 0.9193 (mt) cc_final: 0.8986 (mt) REVERT: C 200 ILE cc_start: 0.8279 (pt) cc_final: 0.7896 (pt) REVERT: C 212 ILE cc_start: 0.6621 (mt) cc_final: 0.6024 (mt) REVERT: C 276 TYR cc_start: 0.8549 (t80) cc_final: 0.8227 (t80) REVERT: D 16 ASP cc_start: 0.4825 (m-30) cc_final: 0.4396 (m-30) REVERT: D 74 MET cc_start: 0.7718 (tpp) cc_final: 0.6931 (ptt) REVERT: D 82 ASP cc_start: 0.8955 (m-30) cc_final: 0.8744 (p0) REVERT: D 242 TYR cc_start: 0.9137 (t80) cc_final: 0.8862 (t80) REVERT: D 262 TYR cc_start: 0.8888 (t80) cc_final: 0.8660 (t80) REVERT: E 25 TRP cc_start: 0.8314 (p-90) cc_final: 0.7970 (p-90) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.1262 time to fit residues: 113.7969 Evaluate side-chains 497 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 390 GLN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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 = 0.4065 r_free = 0.4065 target = 0.153126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107793 restraints weight = 45577.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111839 restraints weight = 27608.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114573 restraints weight = 18766.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116446 restraints weight = 13987.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117721 restraints weight = 11126.821| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17041 Z= 0.147 Angle : 0.663 11.509 23026 Z= 0.350 Chirality : 0.045 0.195 2464 Planarity : 0.003 0.038 2931 Dihedral : 7.882 137.485 2373 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 2012 helix: 0.83 (0.15), residues: 1178 sheet: -0.30 (0.41), residues: 169 loop : -0.13 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.021 0.001 TYR B 471 PHE 0.027 0.002 PHE B 100 TRP 0.011 0.001 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (17038) covalent geometry : angle 0.65945 / 0.35 (23020) SS BOND : bond 0.00564 / 0.28 ( 3) SS BOND : angle 4.53248 / 2.15 ( 6) hydrogen bonds : bond 0.04008 / 2.56 ( 912) hydrogen bonds : angle 5.08109 / 3.58 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8090 (ttp80) REVERT: A 186 ILE cc_start: 0.9565 (mm) cc_final: 0.9354 (mm) REVERT: A 188 ILE cc_start: 0.9554 (mt) cc_final: 0.9197 (mt) REVERT: A 190 MET cc_start: 0.9351 (mtm) cc_final: 0.8979 (mtm) REVERT: A 191 GLN cc_start: 0.8105 (mt0) cc_final: 0.7097 (mt0) REVERT: A 214 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8863 (mmmt) REVERT: A 250 TYR cc_start: 0.7260 (m-80) cc_final: 0.6830 (m-80) REVERT: A 255 HIS cc_start: 0.8350 (t-90) cc_final: 0.7631 (t70) REVERT: A 257 ASP cc_start: 0.8849 (m-30) cc_final: 0.8442 (m-30) REVERT: A 290 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8886 (tm-30) REVERT: A 291 LEU cc_start: 0.9622 (mp) cc_final: 0.9024 (mt) REVERT: A 301 PHE cc_start: 0.8688 (m-80) cc_final: 0.8370 (m-80) REVERT: A 366 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8863 (ptpp) REVERT: A 420 MET cc_start: 0.8836 (tpt) cc_final: 0.8617 (tpt) REVERT: A 447 ASN cc_start: 0.9067 (m-40) cc_final: 0.8586 (t0) REVERT: A 456 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8910 (mtmm) REVERT: A 474 GLN cc_start: 0.8958 (mm110) cc_final: 0.8325 (mp10) REVERT: A 493 MET cc_start: 0.8533 (ttt) cc_final: 0.7722 (ttp) REVERT: A 494 MET cc_start: 0.8279 (mmt) cc_final: 0.7650 (mmt) REVERT: A 501 GLN cc_start: 0.9430 (tt0) cc_final: 0.9038 (tm-30) REVERT: A 510 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8544 (tptp) REVERT: A 586 TYR cc_start: 0.9109 (m-80) cc_final: 0.8761 (m-80) REVERT: A 667 LEU cc_start: 0.9612 (tt) cc_final: 0.9409 (tt) REVERT: A 686 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7834 (mmm160) REVERT: B 10 ILE cc_start: 0.9720 (mt) cc_final: 0.9386 (tp) REVERT: B 40 TYR cc_start: 0.9087 (t80) cc_final: 0.8739 (t80) REVERT: B 95 MET cc_start: 0.8731 (tpp) cc_final: 0.8411 (tpp) REVERT: B 99 LYS cc_start: 0.9460 (tptp) cc_final: 0.9195 (tptp) REVERT: B 150 GLN cc_start: 0.9234 (tp40) cc_final: 0.8976 (tp40) REVERT: B 167 LEU cc_start: 0.8820 (mt) cc_final: 0.8495 (mt) REVERT: B 174 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7734 (tp30) REVERT: B 227 MET cc_start: 0.9199 (ptp) cc_final: 0.8636 (ptp) REVERT: B 235 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8074 (mtm-85) REVERT: B 274 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8390 (mmm160) REVERT: B 314 MET cc_start: 0.8801 (ttp) cc_final: 0.8263 (tmm) REVERT: B 321 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 322 MET cc_start: 0.8524 (mmm) cc_final: 0.7808 (mmm) REVERT: B 348 MET cc_start: 0.8531 (tpt) cc_final: 0.8143 (tpp) REVERT: B 350 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8482 (mmm160) REVERT: B 352 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6786 (mm-30) REVERT: B 375 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8401 (mtpt) REVERT: B 390 GLN cc_start: 0.9277 (mt0) cc_final: 0.9057 (mm-40) REVERT: B 399 GLU cc_start: 0.8903 (tp30) cc_final: 0.8429 (tp30) REVERT: B 403 ILE cc_start: 0.9018 (mm) cc_final: 0.8404 (tp) REVERT: B 456 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8586 (mmtm) REVERT: B 475 ASN cc_start: 0.9133 (m-40) cc_final: 0.8929 (m110) REVERT: B 483 GLU cc_start: 0.9317 (pm20) cc_final: 0.9068 (pm20) REVERT: B 494 MET cc_start: 0.9130 (ttm) cc_final: 0.8800 (mmt) REVERT: B 496 ASN cc_start: 0.9435 (t0) cc_final: 0.9096 (t0) REVERT: B 500 ILE cc_start: 0.9705 (mt) cc_final: 0.9469 (mt) REVERT: B 570 MET cc_start: 0.8447 (tpp) cc_final: 0.7915 (tpp) REVERT: B 571 TYR cc_start: 0.8803 (t80) cc_final: 0.8537 (t80) REVERT: B 575 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7039 (ptp-170) REVERT: B 598 MET cc_start: 0.8529 (ttm) cc_final: 0.8262 (ttm) REVERT: B 602 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 604 ARG cc_start: 0.9393 (mmp80) cc_final: 0.9067 (mmp80) REVERT: B 645 GLN cc_start: 0.9257 (tp40) cc_final: 0.8813 (tp40) REVERT: B 652 ILE cc_start: 0.9146 (mt) cc_final: 0.8911 (mt) REVERT: B 677 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8701 (mmm-85) REVERT: C 200 ILE cc_start: 0.8215 (pt) cc_final: 0.7797 (pt) REVERT: C 276 TYR cc_start: 0.8490 (t80) cc_final: 0.8118 (t80) REVERT: D 74 MET cc_start: 0.7675 (tpp) cc_final: 0.6984 (ptt) REVERT: D 242 TYR cc_start: 0.9119 (t80) cc_final: 0.8823 (t80) REVERT: D 262 TYR cc_start: 0.8882 (t80) cc_final: 0.8637 (t80) REVERT: E 25 TRP cc_start: 0.8316 (p-90) cc_final: 0.8013 (p-90) outliers start: 0 outliers final: 0 residues processed: 575 average time/residue: 0.1304 time to fit residues: 113.9411 Evaluate side-chains 503 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 183 optimal weight: 30.0000 chunk 194 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 312 GLN A 390 GLN A 647 HIS B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.151309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107392 restraints weight = 46243.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110964 restraints weight = 28547.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113538 restraints weight = 20067.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115260 restraints weight = 14965.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116388 restraints weight = 11985.716| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17041 Z= 0.162 Angle : 0.696 11.066 23026 Z= 0.367 Chirality : 0.046 0.407 2464 Planarity : 0.004 0.069 2931 Dihedral : 7.872 138.506 2373 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2012 helix: 0.81 (0.15), residues: 1170 sheet: -0.33 (0.41), residues: 165 loop : -0.18 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.024 0.002 TYR B 471 PHE 0.026 0.002 PHE B 100 TRP 0.011 0.001 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (17038) covalent geometry : angle 0.69086 / 0.36 (23020) SS BOND : bond 0.00720 / 0.34 ( 3) SS BOND : angle 5.12873 / 2.44 ( 6) hydrogen bonds : bond 0.04010 / 2.56 ( 912) hydrogen bonds : angle 5.14174 / 3.65 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.9444 (pt0) cc_final: 0.9206 (pt0) REVERT: A 147 GLN cc_start: 0.9014 (tt0) cc_final: 0.8565 (tp-100) REVERT: A 164 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8193 (ttp80) REVERT: A 186 ILE cc_start: 0.9553 (mm) cc_final: 0.9347 (mm) REVERT: A 188 ILE cc_start: 0.9554 (mt) cc_final: 0.9195 (mt) REVERT: A 190 MET cc_start: 0.9361 (mtm) cc_final: 0.8988 (mtm) REVERT: A 214 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8935 (mmmt) REVERT: A 236 TYR cc_start: 0.9034 (t80) cc_final: 0.8760 (t80) REVERT: A 250 TYR cc_start: 0.7242 (m-80) cc_final: 0.6799 (m-80) REVERT: A 255 HIS cc_start: 0.8393 (t-90) cc_final: 0.7787 (t70) REVERT: A 257 ASP cc_start: 0.8804 (m-30) cc_final: 0.8371 (m-30) REVERT: A 290 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 291 LEU cc_start: 0.9630 (mp) cc_final: 0.9019 (mt) REVERT: A 301 PHE cc_start: 0.8731 (m-80) cc_final: 0.8443 (m-80) REVERT: A 317 MET cc_start: 0.8816 (mmp) cc_final: 0.8535 (mmm) REVERT: A 366 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8874 (ptpp) REVERT: A 456 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8956 (ptpp) REVERT: A 474 GLN cc_start: 0.8988 (mm110) cc_final: 0.8757 (tm-30) REVERT: A 493 MET cc_start: 0.8439 (ttt) cc_final: 0.7844 (ttp) REVERT: A 501 GLN cc_start: 0.9434 (tt0) cc_final: 0.9032 (tm-30) REVERT: A 586 TYR cc_start: 0.9045 (m-80) cc_final: 0.8744 (m-80) REVERT: A 588 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8430 (tp-100) REVERT: A 615 MET cc_start: 0.8967 (mmp) cc_final: 0.8511 (mmp) REVERT: A 667 LEU cc_start: 0.9622 (tt) cc_final: 0.9403 (tt) REVERT: A 686 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7664 (mmm160) REVERT: B 10 ILE cc_start: 0.9716 (mt) cc_final: 0.9394 (tp) REVERT: B 40 TYR cc_start: 0.9117 (t80) cc_final: 0.8769 (t80) REVERT: B 99 LYS cc_start: 0.9462 (tptp) cc_final: 0.9082 (tptm) REVERT: B 129 PHE cc_start: 0.9430 (m-10) cc_final: 0.8878 (m-80) REVERT: B 167 LEU cc_start: 0.8859 (mt) cc_final: 0.8557 (mt) REVERT: B 174 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7740 (tp30) REVERT: B 227 MET cc_start: 0.9105 (ptp) cc_final: 0.8636 (ptp) REVERT: B 235 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: B 274 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8409 (mmm160) REVERT: B 322 MET cc_start: 0.8546 (mmm) cc_final: 0.8284 (mmm) REVERT: B 350 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8527 (mmm160) REVERT: B 375 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8442 (mtpt) REVERT: B 390 GLN cc_start: 0.9284 (mt0) cc_final: 0.9058 (mm-40) REVERT: B 399 GLU cc_start: 0.8958 (tp30) cc_final: 0.8420 (tp30) REVERT: B 403 ILE cc_start: 0.9035 (mm) cc_final: 0.8394 (tp) REVERT: B 456 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8563 (mmtm) REVERT: B 494 MET cc_start: 0.9139 (ttm) cc_final: 0.8859 (mmt) REVERT: B 496 ASN cc_start: 0.9447 (t0) cc_final: 0.9122 (t0) REVERT: B 500 ILE cc_start: 0.9710 (mt) cc_final: 0.9472 (mt) REVERT: B 570 MET cc_start: 0.8549 (tpp) cc_final: 0.8059 (tpp) REVERT: B 571 TYR cc_start: 0.8884 (t80) cc_final: 0.8638 (t80) REVERT: B 575 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7109 (ptp-170) REVERT: B 645 GLN cc_start: 0.9265 (tp40) cc_final: 0.8827 (tp40) REVERT: B 652 ILE cc_start: 0.9192 (mt) cc_final: 0.8966 (mt) REVERT: B 657 PHE cc_start: 0.8852 (m-80) cc_final: 0.8441 (m-80) REVERT: B 677 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8743 (mmm-85) REVERT: C 95 MET cc_start: -0.0152 (ppp) cc_final: -0.0431 (ppp) REVERT: C 157 MET cc_start: 0.8473 (mtm) cc_final: 0.8260 (mtm) REVERT: C 200 ILE cc_start: 0.8012 (pt) cc_final: 0.7667 (pt) REVERT: C 276 TYR cc_start: 0.8506 (t80) cc_final: 0.8127 (t80) REVERT: D 74 MET cc_start: 0.7767 (tpp) cc_final: 0.6958 (ptt) REVERT: D 242 TYR cc_start: 0.9130 (t80) cc_final: 0.8809 (t80) REVERT: D 262 TYR cc_start: 0.8935 (t80) cc_final: 0.8717 (t80) REVERT: E 25 TRP cc_start: 0.8256 (p-90) cc_final: 0.7947 (p-90) REVERT: E 93 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6802 (mmmt) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.1252 time to fit residues: 110.5626 Evaluate side-chains 505 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 390 GLN A 647 HIS B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.153720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109240 restraints weight = 45451.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113170 restraints weight = 28215.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115765 restraints weight = 19354.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117567 restraints weight = 14484.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118776 restraints weight = 11620.112| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17041 Z= 0.148 Angle : 0.692 11.122 23026 Z= 0.364 Chirality : 0.045 0.199 2464 Planarity : 0.003 0.038 2931 Dihedral : 7.836 138.292 2373 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 2012 helix: 0.85 (0.15), residues: 1165 sheet: -0.78 (0.39), residues: 173 loop : -0.24 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 161 TYR 0.023 0.002 TYR B 471 PHE 0.024 0.002 PHE B 100 TRP 0.014 0.001 TRP D 30 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (17038) covalent geometry : angle 0.68816 / 0.36 (23020) SS BOND : bond 0.00820 / 0.41 ( 3) SS BOND : angle 4.47174 / 2.14 ( 6) hydrogen bonds : bond 0.03940 / 2.52 ( 912) hydrogen bonds : angle 5.12012 / 3.61 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3587.89 seconds wall clock time: 62 minutes 59.16 seconds (3779.16 seconds total)