Starting phenix.real_space_refine on Fri Jul 3 22:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxx_45014/07_2026/9bxx_45014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxx_45014/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bxx_45014/07_2026/9bxx_45014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxx_45014/07_2026/9bxx_45014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxx_45014/07_2026/9bxx_45014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxx_45014/07_2026/9bxx_45014.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.60, per 1000 atoms: 0.22 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: 1.27 Conformation dependent library (CDL) restraints added in 835.5 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: 0.48 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: 2.71 Time building geometry restraints manager: 1.69 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 3.060 ... (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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- 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 : 0.622 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: 0.1404 time to fit residues: 180.6397 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 : 0.614 ------------------------------------------------------------------------------- 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 ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 34 HIS B 61 ASN B 304 HIS B 447 ASN C 24 GLN C 28 GLN D 71 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104451 restraints weight = 43792.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108645 restraints weight = 26587.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111378 restraints weight = 17980.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113275 restraints weight = 13527.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114626 restraints weight = 10805.148| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (20 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17041 Z= 0.257 Angle : 0.728 15.163 23026 Z= 0.385 Chirality : 0.046 0.261 2464 Planarity : 0.005 0.057 2931 Dihedral : 9.215 138.683 2373 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.34 % Allowed : 3.69 % Favored : 95.98 % 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: 0.98 (0.18), residues: 2012 helix: 1.10 (0.15), residues: 1160 sheet: -0.37 (0.35), residues: 177 loop : 0.39 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.036 0.002 TYR B 36 PHE 0.027 0.003 PHE A 492 TRP 0.023 0.002 TRP B 558 HIS 0.010 0.002 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.26 (17038) covalent geometry : angle 0.71787 / 0.38 (23020) SS BOND : bond 0.01135 / 0.54 ( 3) SS BOND : angle 7.61308 / 3.79 ( 6) hydrogen bonds : bond 0.05150 / 3.39 ( 912) hydrogen bonds : angle 5.30746 / 3.67 ( 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 656 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 650 time to evaluate : 0.546 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: A 81 PHE cc_start: 0.9382 (m-80) cc_final: 0.9048 (m-80) REVERT: A 99 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9337 (tppp) REVERT: A 147 GLN cc_start: 0.9140 (mt0) cc_final: 0.8569 (mt0) REVERT: A 186 ILE cc_start: 0.9547 (mm) cc_final: 0.9248 (mm) REVERT: A 190 MET cc_start: 0.9298 (mtm) cc_final: 0.8973 (mtm) REVERT: A 250 TYR cc_start: 0.7219 (m-80) cc_final: 0.6838 (m-80) REVERT: A 257 ASP cc_start: 0.8675 (m-30) cc_final: 0.8053 (m-30) REVERT: A 262 LEU cc_start: 0.9638 (mt) cc_final: 0.9415 (mt) REVERT: A 263 ASP cc_start: 0.8957 (m-30) cc_final: 0.8586 (m-30) REVERT: A 301 PHE cc_start: 0.8901 (m-80) cc_final: 0.8169 (m-10) REVERT: A 312 GLN cc_start: 0.8809 (tp40) cc_final: 0.8326 (tp40) REVERT: A 316 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 362 ASP cc_start: 0.8443 (m-30) cc_final: 0.7879 (m-30) REVERT: A 466 MET cc_start: 0.9047 (ptt) cc_final: 0.8735 (ptt) REVERT: A 475 ASN cc_start: 0.8879 (m-40) cc_final: 0.8553 (m110) REVERT: A 501 GLN cc_start: 0.9439 (tt0) cc_final: 0.8980 (tm-30) REVERT: A 516 GLN cc_start: 0.9278 (tt0) cc_final: 0.8874 (tt0) REVERT: A 571 TYR cc_start: 0.8673 (t80) cc_final: 0.8225 (t80) REVERT: A 628 GLU cc_start: 0.9275 (tt0) cc_final: 0.8991 (tt0) REVERT: A 632 MET cc_start: 0.8328 (mtt) cc_final: 0.8028 (mtm) REVERT: A 645 GLN cc_start: 0.8606 (tp40) cc_final: 0.8108 (tp40) REVERT: A 650 GLN cc_start: 0.8360 (mt0) cc_final: 0.7416 (mt0) REVERT: A 664 THR cc_start: 0.9339 (p) cc_final: 0.8821 (p) REVERT: A 668 ASN cc_start: 0.9034 (m-40) cc_final: 0.8423 (m-40) REVERT: A 686 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7381 (tpt90) REVERT: B 23 LYS cc_start: 0.9422 (mmtm) cc_final: 0.9018 (mmmt) REVERT: B 128 PHE cc_start: 0.9677 (t80) cc_final: 0.9460 (t80) REVERT: B 139 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8860 (mt-10) REVERT: B 144 MET cc_start: 0.9355 (mtm) cc_final: 0.8649 (mtm) REVERT: B 145 ILE cc_start: 0.9439 (tp) cc_final: 0.8955 (tp) REVERT: B 147 GLN cc_start: 0.9400 (mt0) cc_final: 0.9174 (mp10) REVERT: B 172 LEU cc_start: 0.8801 (mp) cc_final: 0.8526 (mp) REVERT: B 184 ARG cc_start: 0.8896 (mtt180) cc_final: 0.8358 (ttm170) REVERT: B 186 ILE cc_start: 0.9712 (mt) cc_final: 0.9464 (mt) REVERT: B 190 MET cc_start: 0.9441 (mtm) cc_final: 0.8922 (mtm) REVERT: B 239 GLN cc_start: 0.7687 (mt0) cc_final: 0.7081 (mm-40) REVERT: B 250 TYR cc_start: 0.8287 (m-80) cc_final: 0.7940 (m-80) REVERT: B 335 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7944 (mt-10) REVERT: B 348 MET cc_start: 0.8554 (tpt) cc_final: 0.8247 (tpp) REVERT: B 375 LYS cc_start: 0.8412 (mmmm) cc_final: 0.8139 (mmmm) REVERT: B 377 LYS cc_start: 0.7753 (mttt) cc_final: 0.7506 (mttt) REVERT: B 403 ILE cc_start: 0.9285 (mm) cc_final: 0.9065 (mm) REVERT: B 416 ILE cc_start: 0.9092 (mm) cc_final: 0.8833 (mm) REVERT: B 420 MET cc_start: 0.9024 (mmm) cc_final: 0.8758 (mmp) REVERT: B 425 ILE cc_start: 0.9351 (mt) cc_final: 0.9100 (mt) REVERT: B 496 ASN cc_start: 0.9406 (t0) cc_final: 0.9055 (t0) REVERT: B 501 GLN cc_start: 0.9532 (tt0) cc_final: 0.9249 (tt0) REVERT: B 576 LEU cc_start: 0.9248 (mt) cc_final: 0.9029 (mt) REVERT: B 604 ARG cc_start: 0.9326 (mmp80) cc_final: 0.8783 (mmp80) REVERT: B 640 MET cc_start: 0.9143 (tpp) cc_final: 0.8862 (tpp) REVERT: B 645 GLN cc_start: 0.9199 (tp40) cc_final: 0.8928 (tp-100) REVERT: B 650 GLN cc_start: 0.6680 (mt0) cc_final: 0.5930 (mt0) REVERT: B 686 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8097 (mmm160) REVERT: C 33 GLU cc_start: 0.4539 (mp0) cc_final: 0.4146 (pp20) REVERT: C 157 MET cc_start: 0.8678 (mtm) cc_final: 0.8233 (mtm) REVERT: C 162 TYR cc_start: 0.7724 (m-80) cc_final: 0.7489 (m-10) REVERT: C 177 TYR cc_start: 0.8959 (t80) cc_final: 0.8640 (t80) REVERT: D 82 ASP cc_start: 0.8839 (m-30) cc_final: 0.8429 (p0) REVERT: D 137 MET cc_start: 0.5849 (ttt) cc_final: 0.5307 (tmm) REVERT: D 179 TYR cc_start: 0.8170 (t80) cc_final: 0.7870 (t80) REVERT: D 242 TYR cc_start: 0.9027 (t80) cc_final: 0.8554 (t80) REVERT: D 262 TYR cc_start: 0.8600 (t80) cc_final: 0.8320 (t80) REVERT: E 60 ASN cc_start: 0.8482 (m-40) cc_final: 0.8228 (p0) outliers start: 6 outliers final: 1 residues processed: 652 average time/residue: 0.1305 time to fit residues: 128.4130 Evaluate side-chains 529 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 467 ASN A 568 HIS B 11 GLN B 313 HIS B 447 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106384 restraints weight = 44687.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110412 restraints weight = 27401.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113160 restraints weight = 18726.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115037 restraints weight = 13934.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116292 restraints weight = 11120.194| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17041 Z= 0.148 Angle : 0.613 8.569 23026 Z= 0.324 Chirality : 0.043 0.228 2464 Planarity : 0.004 0.043 2931 Dihedral : 8.914 134.151 2373 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.17 % Allowed : 2.79 % Favored : 97.04 % 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: 1.14 (0.18), residues: 2012 helix: 1.22 (0.15), residues: 1160 sheet: 0.37 (0.43), residues: 143 loop : 0.25 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.028 0.002 TYR B 36 PHE 0.042 0.002 PHE C 92 TRP 0.009 0.001 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (17038) covalent geometry : angle 0.61020 / 0.32 (23020) SS BOND : bond 0.01302 / 0.64 ( 3) SS BOND : angle 3.47234 / 1.72 ( 6) hydrogen bonds : bond 0.04411 / 2.85 ( 912) hydrogen bonds : angle 5.00998 / 3.48 ( 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 657 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 654 time to evaluate : 0.635 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: A 96 SER cc_start: 0.8805 (m) cc_final: 0.8567 (t) REVERT: A 142 ASN cc_start: 0.9259 (m-40) cc_final: 0.8974 (m110) REVERT: A 147 GLN cc_start: 0.9168 (mt0) cc_final: 0.7821 (mt0) REVERT: A 186 ILE cc_start: 0.9543 (mm) cc_final: 0.9193 (mm) REVERT: A 188 ILE cc_start: 0.9563 (mt) cc_final: 0.9231 (mt) REVERT: A 190 MET cc_start: 0.9316 (mtm) cc_final: 0.9012 (mtm) REVERT: A 250 TYR cc_start: 0.7310 (m-80) cc_final: 0.6830 (m-80) REVERT: A 257 ASP cc_start: 0.8690 (m-30) cc_final: 0.8244 (m-30) REVERT: A 263 ASP cc_start: 0.9052 (m-30) cc_final: 0.8671 (m-30) REVERT: A 291 LEU cc_start: 0.9653 (mp) cc_final: 0.9305 (mp) REVERT: A 301 PHE cc_start: 0.8858 (m-80) cc_final: 0.8341 (m-80) REVERT: A 312 GLN cc_start: 0.8661 (tp40) cc_final: 0.8349 (tp40) REVERT: A 316 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 317 MET cc_start: 0.9054 (mmm) cc_final: 0.8801 (mmm) REVERT: A 320 ASN cc_start: 0.8606 (m-40) cc_final: 0.8190 (m-40) REVERT: A 322 MET cc_start: 0.8937 (mmm) cc_final: 0.8671 (mmm) REVERT: A 352 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 393 SER cc_start: 0.9105 (t) cc_final: 0.8466 (t) REVERT: A 402 GLU cc_start: 0.8037 (mp0) cc_final: 0.7466 (mp0) REVERT: A 475 ASN cc_start: 0.8824 (m-40) cc_final: 0.8404 (m110) REVERT: A 501 GLN cc_start: 0.9425 (tt0) cc_final: 0.8964 (tm-30) REVERT: A 509 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8857 (tm-30) REVERT: A 588 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8055 (mm-40) REVERT: A 601 ILE cc_start: 0.9448 (tt) cc_final: 0.9154 (tt) REVERT: A 615 MET cc_start: 0.8964 (mmp) cc_final: 0.8672 (mmp) REVERT: A 628 GLU cc_start: 0.9246 (tt0) cc_final: 0.8815 (tt0) REVERT: A 645 GLN cc_start: 0.8567 (tp40) cc_final: 0.8162 (tp40) REVERT: A 650 GLN cc_start: 0.8422 (mt0) cc_final: 0.7971 (mt0) REVERT: A 664 THR cc_start: 0.9365 (p) cc_final: 0.8814 (p) REVERT: A 668 ASN cc_start: 0.8896 (m-40) cc_final: 0.8443 (m-40) REVERT: A 686 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7369 (mmm160) REVERT: B 10 ILE cc_start: 0.9727 (mt) cc_final: 0.9448 (tp) REVERT: B 18 ILE cc_start: 0.9281 (mm) cc_final: 0.9024 (mm) REVERT: B 23 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8947 (mmmt) REVERT: B 25 GLN cc_start: 0.8822 (mt0) cc_final: 0.8560 (mt0) REVERT: B 99 LYS cc_start: 0.9334 (tptm) cc_final: 0.9005 (tptm) REVERT: B 144 MET cc_start: 0.9221 (mtm) cc_final: 0.8947 (mtm) REVERT: B 172 LEU cc_start: 0.8835 (mp) cc_final: 0.8587 (mp) REVERT: B 184 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8585 (ttm-80) REVERT: B 186 ILE cc_start: 0.9734 (mt) cc_final: 0.9436 (mt) REVERT: B 190 MET cc_start: 0.9396 (mtm) cc_final: 0.9138 (mtm) REVERT: B 312 GLN cc_start: 0.8660 (tt0) cc_final: 0.8220 (tt0) REVERT: B 317 MET cc_start: 0.8608 (mtt) cc_final: 0.8354 (mtm) REVERT: B 319 MET cc_start: 0.8561 (tpp) cc_final: 0.8167 (tpp) REVERT: B 335 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 349 LEU cc_start: 0.9585 (mt) cc_final: 0.9363 (mt) REVERT: B 375 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8012 (mmmm) REVERT: B 390 GLN cc_start: 0.9244 (mt0) cc_final: 0.8964 (mm-40) REVERT: B 403 ILE cc_start: 0.9186 (mm) cc_final: 0.8938 (mm) REVERT: B 496 ASN cc_start: 0.9379 (t0) cc_final: 0.8801 (t0) REVERT: B 501 GLN cc_start: 0.9511 (tt0) cc_final: 0.9278 (tt0) REVERT: B 516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8680 (tp-100) REVERT: B 528 PHE cc_start: 0.9284 (m-80) cc_final: 0.9059 (m-80) REVERT: B 604 ARG cc_start: 0.9276 (mmp80) cc_final: 0.8953 (mmp80) REVERT: B 636 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9148 (mmmt) REVERT: B 640 MET cc_start: 0.9104 (tpp) cc_final: 0.8831 (tpp) REVERT: B 645 GLN cc_start: 0.9207 (tp40) cc_final: 0.8918 (tp-100) REVERT: B 650 GLN cc_start: 0.6870 (mt0) cc_final: 0.6621 (mt0) REVERT: B 664 THR cc_start: 0.8877 (p) cc_final: 0.8591 (t) REVERT: C 157 MET cc_start: 0.8208 (mtm) cc_final: 0.7669 (mtm) REVERT: C 162 TYR cc_start: 0.7739 (m-80) cc_final: 0.7528 (m-10) REVERT: C 177 TYR cc_start: 0.8984 (t80) cc_final: 0.8630 (t80) REVERT: C 197 ASP cc_start: 0.7987 (m-30) cc_final: 0.6454 (m-30) REVERT: C 237 GLU cc_start: 0.9626 (mp0) cc_final: 0.9404 (pp20) REVERT: D 82 ASP cc_start: 0.8877 (m-30) cc_final: 0.8300 (p0) REVERT: D 137 MET cc_start: 0.6088 (ttt) cc_final: 0.5704 (tmm) REVERT: D 227 PHE cc_start: 0.6937 (t80) cc_final: 0.6630 (t80) REVERT: D 235 LEU cc_start: 0.7534 (mp) cc_final: 0.7133 (mt) REVERT: D 242 TYR cc_start: 0.9035 (t80) cc_final: 0.8818 (t80) REVERT: D 262 TYR cc_start: 0.8683 (t80) cc_final: 0.8410 (t80) REVERT: D 265 ASN cc_start: -0.0227 (m-40) cc_final: -0.0447 (t0) REVERT: E 25 TRP cc_start: 0.8349 (p-90) cc_final: 0.7523 (p-90) REVERT: E 34 MET cc_start: 0.9003 (mpp) cc_final: 0.8766 (ptp) outliers start: 3 outliers final: 1 residues processed: 655 average time/residue: 0.1281 time to fit residues: 125.6700 Evaluate side-chains 529 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 0.7980 chunk 145 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 180 ASN A 232 ASN A 475 ASN B 646 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107151 restraints weight = 44978.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111126 restraints weight = 27520.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113821 restraints weight = 18693.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115588 restraints weight = 13812.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116888 restraints weight = 11005.181| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17041 Z= 0.159 Angle : 0.616 9.937 23026 Z= 0.327 Chirality : 0.043 0.222 2464 Planarity : 0.004 0.038 2931 Dihedral : 8.815 134.925 2373 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % 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: 1.04 (0.18), residues: 2012 helix: 1.20 (0.15), residues: 1162 sheet: -0.32 (0.38), residues: 187 loop : 0.28 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 575 TYR 0.023 0.002 TYR B 36 PHE 0.025 0.002 PHE A 492 TRP 0.007 0.001 TRP A 623 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (17038) covalent geometry : angle 0.61092 / 0.32 (23020) SS BOND : bond 0.01239 / 0.59 ( 3) SS BOND : angle 4.71993 / 2.25 ( 6) hydrogen bonds : bond 0.04173 / 2.68 ( 912) hydrogen bonds : angle 4.95668 / 3.45 ( 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 616 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 614 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 186 ILE cc_start: 0.9554 (mm) cc_final: 0.9213 (mm) REVERT: A 188 ILE cc_start: 0.9561 (mt) cc_final: 0.9220 (mt) REVERT: A 190 MET cc_start: 0.9298 (mtm) cc_final: 0.9036 (mtm) REVERT: A 223 VAL cc_start: 0.9107 (p) cc_final: 0.8872 (p) REVERT: A 250 TYR cc_start: 0.7280 (m-80) cc_final: 0.6826 (m-80) REVERT: A 255 HIS cc_start: 0.8263 (t-90) cc_final: 0.7786 (t70) REVERT: A 257 ASP cc_start: 0.8654 (m-30) cc_final: 0.8406 (m-30) REVERT: A 263 ASP cc_start: 0.9071 (m-30) cc_final: 0.8714 (m-30) REVERT: A 290 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 291 LEU cc_start: 0.9655 (mp) cc_final: 0.9191 (mt) REVERT: A 301 PHE cc_start: 0.8791 (m-80) cc_final: 0.8363 (m-80) REVERT: A 312 GLN cc_start: 0.8664 (tp40) cc_final: 0.8341 (tp40) REVERT: A 316 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 317 MET cc_start: 0.9067 (mmm) cc_final: 0.8823 (mmm) REVERT: A 320 ASN cc_start: 0.8614 (m-40) cc_final: 0.8177 (m-40) REVERT: A 322 MET cc_start: 0.8840 (mmm) cc_final: 0.8576 (mmm) REVERT: A 350 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7861 (mtp85) REVERT: A 494 MET cc_start: 0.8525 (mmp) cc_final: 0.7879 (mmt) REVERT: A 501 GLN cc_start: 0.9437 (tt0) cc_final: 0.9031 (tm-30) REVERT: A 510 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8438 (tptp) REVERT: A 586 TYR cc_start: 0.9142 (m-80) cc_final: 0.8434 (m-80) REVERT: A 588 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8326 (mm-40) REVERT: A 599 GLU cc_start: 0.9046 (pt0) cc_final: 0.8689 (pt0) REVERT: A 601 ILE cc_start: 0.9455 (tt) cc_final: 0.9103 (tt) REVERT: A 615 MET cc_start: 0.9036 (mmp) cc_final: 0.8733 (mmp) REVERT: A 645 GLN cc_start: 0.8601 (tp40) cc_final: 0.8326 (tp40) REVERT: A 664 THR cc_start: 0.9392 (p) cc_final: 0.8906 (p) REVERT: A 668 ASN cc_start: 0.8935 (m-40) cc_final: 0.8581 (m-40) REVERT: A 686 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7717 (mmm160) REVERT: B 23 LYS cc_start: 0.9324 (mmtm) cc_final: 0.8938 (mmmt) REVERT: B 95 MET cc_start: 0.8787 (tpp) cc_final: 0.8527 (tpp) REVERT: B 99 LYS cc_start: 0.9452 (tptm) cc_final: 0.8957 (tptm) REVERT: B 119 GLU cc_start: 0.9369 (pm20) cc_final: 0.8989 (pm20) REVERT: B 124 ILE cc_start: 0.9561 (mm) cc_final: 0.9065 (mm) REVERT: B 128 PHE cc_start: 0.9646 (t80) cc_final: 0.9438 (t80) REVERT: B 150 GLN cc_start: 0.9269 (tp40) cc_final: 0.9060 (tp40) REVERT: B 158 ASN cc_start: 0.9089 (m-40) cc_final: 0.8293 (p0) REVERT: B 172 LEU cc_start: 0.8811 (mp) cc_final: 0.8533 (mp) REVERT: B 184 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8443 (ttm-80) REVERT: B 190 MET cc_start: 0.9356 (mtm) cc_final: 0.9108 (mtm) REVERT: B 335 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 348 MET cc_start: 0.8386 (tpt) cc_final: 0.8131 (tpp) REVERT: B 399 GLU cc_start: 0.8988 (tp30) cc_final: 0.8446 (tp30) REVERT: B 403 ILE cc_start: 0.9187 (mm) cc_final: 0.8906 (mm) REVERT: B 426 GLU cc_start: 0.9064 (tp30) cc_final: 0.8828 (mm-30) REVERT: B 430 LYS cc_start: 0.9040 (mttt) cc_final: 0.8821 (mmtt) REVERT: B 475 ASN cc_start: 0.9264 (m-40) cc_final: 0.9028 (m110) REVERT: B 496 ASN cc_start: 0.9411 (t0) cc_final: 0.9100 (t0) REVERT: B 501 GLN cc_start: 0.9516 (tt0) cc_final: 0.9204 (tt0) REVERT: B 576 LEU cc_start: 0.9398 (mt) cc_final: 0.9186 (mt) REVERT: B 598 MET cc_start: 0.8735 (ttp) cc_final: 0.8492 (ttp) REVERT: B 640 MET cc_start: 0.9008 (tpp) cc_final: 0.8758 (tpp) REVERT: B 645 GLN cc_start: 0.9232 (tp40) cc_final: 0.8809 (tp40) REVERT: B 650 GLN cc_start: 0.6598 (mt0) cc_final: 0.6003 (mt0) REVERT: C 157 MET cc_start: 0.8277 (mtm) cc_final: 0.7777 (mtm) REVERT: C 177 TYR cc_start: 0.8979 (t80) cc_final: 0.8740 (t80) REVERT: C 200 ILE cc_start: 0.8406 (pt) cc_final: 0.8181 (pt) REVERT: C 204 TYR cc_start: 0.8516 (t80) cc_final: 0.8289 (t80) REVERT: C 276 TYR cc_start: 0.8302 (t80) cc_final: 0.7984 (t80) REVERT: D 82 ASP cc_start: 0.8911 (m-30) cc_final: 0.8335 (p0) REVERT: D 137 MET cc_start: 0.6465 (ttt) cc_final: 0.6096 (tmm) REVERT: D 235 LEU cc_start: 0.7310 (mp) cc_final: 0.7074 (mt) REVERT: D 242 TYR cc_start: 0.9069 (t80) cc_final: 0.8760 (t80) REVERT: D 262 TYR cc_start: 0.8697 (t80) cc_final: 0.8370 (t80) REVERT: E 25 TRP cc_start: 0.8384 (p-90) cc_final: 0.7592 (p-90) REVERT: E 34 MET cc_start: 0.9052 (mpp) cc_final: 0.8836 (ptp) outliers start: 2 outliers final: 2 residues processed: 616 average time/residue: 0.1276 time to fit residues: 118.5265 Evaluate side-chains 526 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 524 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 146 optimal weight: 0.0670 chunk 15 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.152488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107345 restraints weight = 44955.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111389 restraints weight = 27642.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114081 restraints weight = 18662.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115903 restraints weight = 13815.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117187 restraints weight = 10978.082| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (17 function evaluations) r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17041 Z= 0.146 Angle : 0.598 8.869 23026 Z= 0.317 Chirality : 0.042 0.183 2464 Planarity : 0.003 0.046 2931 Dihedral : 8.538 133.309 2373 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.60 % 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: 0.97 (0.19), residues: 2012 helix: 1.18 (0.15), residues: 1166 sheet: -0.41 (0.38), residues: 185 loop : 0.19 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 446 TYR 0.024 0.002 TYR D 105 PHE 0.022 0.002 PHE C 227 TRP 0.007 0.001 TRP A 9 HIS 0.007 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (17038) covalent geometry : angle 0.59587 / 0.32 (23020) SS BOND : bond 0.00879 / 0.45 ( 3) SS BOND : angle 3.42849 / 1.67 ( 6) hydrogen bonds : bond 0.03971 / 2.55 ( 912) hydrogen bonds : angle 4.90803 / 3.41 ( 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 595 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.9382 (t80) cc_final: 0.9124 (t80) REVERT: A 147 GLN cc_start: 0.9164 (mt0) cc_final: 0.8667 (mt0) REVERT: A 161 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7619 (ptm160) REVERT: A 186 ILE cc_start: 0.9558 (mm) cc_final: 0.9231 (mm) REVERT: A 188 ILE cc_start: 0.9542 (mt) cc_final: 0.9314 (mt) REVERT: A 250 TYR cc_start: 0.7280 (m-80) cc_final: 0.6814 (m-80) REVERT: A 255 HIS cc_start: 0.8112 (t-90) cc_final: 0.7630 (t70) REVERT: A 257 ASP cc_start: 0.8608 (m-30) cc_final: 0.8140 (m-30) REVERT: A 263 ASP cc_start: 0.9067 (m-30) cc_final: 0.8719 (m-30) REVERT: A 290 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8870 (tm-30) REVERT: A 291 LEU cc_start: 0.9653 (mp) cc_final: 0.9211 (mt) REVERT: A 301 PHE cc_start: 0.8789 (m-80) cc_final: 0.8387 (m-80) REVERT: A 312 GLN cc_start: 0.8760 (tp40) cc_final: 0.8499 (tp40) REVERT: A 316 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 320 ASN cc_start: 0.8620 (m-40) cc_final: 0.8356 (m-40) REVERT: A 322 MET cc_start: 0.8854 (mmm) cc_final: 0.8580 (mmm) REVERT: A 393 SER cc_start: 0.9148 (t) cc_final: 0.8324 (t) REVERT: A 402 GLU cc_start: 0.8210 (mp0) cc_final: 0.7524 (mp0) REVERT: A 403 ILE cc_start: 0.8382 (mm) cc_final: 0.8173 (mm) REVERT: A 447 ASN cc_start: 0.8905 (m-40) cc_final: 0.8610 (m-40) REVERT: A 494 MET cc_start: 0.8526 (mmp) cc_final: 0.8097 (mmp) REVERT: A 501 GLN cc_start: 0.9438 (tt0) cc_final: 0.9095 (tm-30) REVERT: A 510 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8490 (tptp) REVERT: A 599 GLU cc_start: 0.8983 (pt0) cc_final: 0.8684 (pt0) REVERT: A 601 ILE cc_start: 0.9470 (tt) cc_final: 0.9063 (tt) REVERT: A 628 GLU cc_start: 0.9257 (tt0) cc_final: 0.8880 (tt0) REVERT: A 645 GLN cc_start: 0.8602 (tp40) cc_final: 0.8277 (tp-100) REVERT: A 664 THR cc_start: 0.9383 (p) cc_final: 0.8973 (p) REVERT: A 667 LEU cc_start: 0.9331 (tt) cc_final: 0.9113 (tt) REVERT: A 668 ASN cc_start: 0.8984 (m-40) cc_final: 0.8757 (m-40) REVERT: A 686 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7638 (mmm160) REVERT: B 40 TYR cc_start: 0.9174 (t80) cc_final: 0.8861 (t80) REVERT: B 95 MET cc_start: 0.8827 (tpp) cc_final: 0.8545 (tpp) REVERT: B 99 LYS cc_start: 0.9412 (tptm) cc_final: 0.9075 (tptp) REVERT: B 119 GLU cc_start: 0.9377 (pm20) cc_final: 0.8892 (pm20) REVERT: B 120 ASP cc_start: 0.9282 (m-30) cc_final: 0.8997 (m-30) REVERT: B 128 PHE cc_start: 0.9677 (t80) cc_final: 0.9472 (t80) REVERT: B 150 GLN cc_start: 0.9311 (tp40) cc_final: 0.9085 (tp-100) REVERT: B 158 ASN cc_start: 0.9056 (m-40) cc_final: 0.8418 (p0) REVERT: B 184 ARG cc_start: 0.8876 (mtt180) cc_final: 0.8450 (ttm-80) REVERT: B 227 MET cc_start: 0.9251 (ptp) cc_final: 0.8570 (ptp) REVERT: B 235 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.7936 (mtm-85) REVERT: B 335 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8088 (mt-10) REVERT: B 348 MET cc_start: 0.8369 (tpt) cc_final: 0.7946 (tpp) REVERT: B 352 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 375 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8144 (mmmm) REVERT: B 403 ILE cc_start: 0.9118 (mm) cc_final: 0.8863 (mm) REVERT: B 471 TYR cc_start: 0.9230 (t80) cc_final: 0.9027 (t80) REVERT: B 475 ASN cc_start: 0.9223 (m-40) cc_final: 0.8870 (m-40) REVERT: B 494 MET cc_start: 0.8684 (ttm) cc_final: 0.8464 (ttm) REVERT: B 496 ASN cc_start: 0.9416 (t0) cc_final: 0.9098 (t0) REVERT: B 501 GLN cc_start: 0.9552 (tt0) cc_final: 0.9346 (tm-30) REVERT: B 645 GLN cc_start: 0.9178 (tp40) cc_final: 0.8805 (tp40) REVERT: B 650 GLN cc_start: 0.6631 (mt0) cc_final: 0.5996 (mt0) REVERT: B 652 ILE cc_start: 0.9189 (mt) cc_final: 0.8923 (mt) REVERT: B 655 THR cc_start: 0.9062 (t) cc_final: 0.8856 (t) REVERT: C 157 MET cc_start: 0.8331 (mtm) cc_final: 0.7920 (mtm) REVERT: C 177 TYR cc_start: 0.8973 (t80) cc_final: 0.8753 (t80) REVERT: C 200 ILE cc_start: 0.8396 (pt) cc_final: 0.8143 (pt) REVERT: C 212 ILE cc_start: 0.6269 (mt) cc_final: 0.5841 (mt) REVERT: C 317 ASP cc_start: 0.8428 (t0) cc_final: 0.8163 (t0) REVERT: D 82 ASP cc_start: 0.8982 (m-30) cc_final: 0.8636 (p0) REVERT: D 137 MET cc_start: 0.6598 (ttt) cc_final: 0.6282 (tmm) REVERT: D 242 TYR cc_start: 0.9067 (t80) cc_final: 0.8842 (t80) REVERT: D 262 TYR cc_start: 0.8673 (t80) cc_final: 0.8427 (t80) REVERT: E 34 MET cc_start: 0.9096 (mpp) cc_final: 0.8895 (ptt) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 0.1221 time to fit residues: 109.8915 Evaluate side-chains 516 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 6.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 467 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.150542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106175 restraints weight = 45523.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110106 restraints weight = 27852.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112702 restraints weight = 18966.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114494 restraints weight = 14102.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115730 restraints weight = 11226.111| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17041 Z= 0.166 Angle : 0.615 9.859 23026 Z= 0.325 Chirality : 0.043 0.183 2464 Planarity : 0.003 0.041 2931 Dihedral : 8.296 133.812 2373 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.06 % Allowed : 1.68 % 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: 0.89 (0.19), residues: 2012 helix: 1.12 (0.15), residues: 1171 sheet: -0.41 (0.40), residues: 175 loop : 0.13 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 502 TYR 0.016 0.001 TYR D 242 PHE 0.018 0.002 PHE B 100 TRP 0.008 0.001 TRP A 623 HIS 0.007 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (17038) covalent geometry : angle 0.61109 / 0.32 (23020) SS BOND : bond 0.00648 / 0.31 ( 3) SS BOND : angle 4.52178 / 2.14 ( 6) hydrogen bonds : bond 0.03953 / 2.54 ( 912) hydrogen bonds : angle 4.99052 / 3.49 ( 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 594 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 593 time to evaluate : 0.658 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 161 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7237 (ptm160) REVERT: A 164 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8235 (ttm110) REVERT: A 186 ILE cc_start: 0.9558 (mm) cc_final: 0.9331 (mm) REVERT: A 188 ILE cc_start: 0.9573 (mt) cc_final: 0.9342 (mt) REVERT: A 190 MET cc_start: 0.9340 (mtm) cc_final: 0.8990 (mtm) REVERT: A 250 TYR cc_start: 0.7297 (m-80) cc_final: 0.6898 (m-80) REVERT: A 255 HIS cc_start: 0.8018 (t-90) cc_final: 0.7554 (t70) REVERT: A 257 ASP cc_start: 0.8647 (m-30) cc_final: 0.8236 (m-30) REVERT: A 263 ASP cc_start: 0.9094 (m-30) cc_final: 0.8730 (m-30) REVERT: A 290 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8682 (tm-30) REVERT: A 291 LEU cc_start: 0.9666 (mp) cc_final: 0.9177 (mt) REVERT: A 301 PHE cc_start: 0.8744 (m-80) cc_final: 0.8440 (m-80) REVERT: A 312 GLN cc_start: 0.8672 (tp40) cc_final: 0.8433 (tp40) REVERT: A 317 MET cc_start: 0.9001 (mmm) cc_final: 0.8712 (mmm) REVERT: A 322 MET cc_start: 0.8857 (mmm) cc_final: 0.8592 (mmm) REVERT: A 393 SER cc_start: 0.9175 (t) cc_final: 0.8182 (t) REVERT: A 402 GLU cc_start: 0.8320 (mp0) cc_final: 0.7605 (mp0) REVERT: A 447 ASN cc_start: 0.8847 (m-40) cc_final: 0.8537 (m-40) REVERT: A 501 GLN cc_start: 0.9440 (tt0) cc_final: 0.9090 (tm-30) REVERT: A 628 GLU cc_start: 0.9254 (tt0) cc_final: 0.8902 (tt0) REVERT: A 664 THR cc_start: 0.9434 (p) cc_final: 0.9056 (p) REVERT: A 668 ASN cc_start: 0.9136 (m-40) cc_final: 0.8804 (m-40) REVERT: A 686 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7590 (mmm160) REVERT: B 99 LYS cc_start: 0.9406 (tptm) cc_final: 0.8826 (tptm) REVERT: B 118 TYR cc_start: 0.8960 (t80) cc_final: 0.8751 (t80) REVERT: B 119 GLU cc_start: 0.9412 (pm20) cc_final: 0.9024 (pm20) REVERT: B 120 ASP cc_start: 0.9306 (m-30) cc_final: 0.9068 (m-30) REVERT: B 158 ASN cc_start: 0.9047 (m-40) cc_final: 0.8415 (p0) REVERT: B 184 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8705 (ttm-80) REVERT: B 227 MET cc_start: 0.9158 (ptp) cc_final: 0.8622 (ptp) REVERT: B 235 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8165 (mtm-85) REVERT: B 335 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 349 LEU cc_start: 0.9589 (mt) cc_final: 0.9387 (mt) REVERT: B 375 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8128 (mmmm) REVERT: B 399 GLU cc_start: 0.8944 (tp30) cc_final: 0.8387 (tp30) REVERT: B 403 ILE cc_start: 0.9164 (mm) cc_final: 0.8823 (mm) REVERT: B 494 MET cc_start: 0.9030 (ttm) cc_final: 0.8821 (ttm) REVERT: B 496 ASN cc_start: 0.9439 (t0) cc_final: 0.9120 (t0) REVERT: B 570 MET cc_start: 0.8822 (tpp) cc_final: 0.8225 (tpp) REVERT: B 586 TYR cc_start: 0.9516 (m-80) cc_final: 0.9215 (m-80) REVERT: B 598 MET cc_start: 0.8693 (ttm) cc_final: 0.8372 (ttm) REVERT: B 645 GLN cc_start: 0.9211 (tp40) cc_final: 0.8835 (tp40) REVERT: B 650 GLN cc_start: 0.6517 (mt0) cc_final: 0.5952 (mt0) REVERT: B 652 ILE cc_start: 0.9171 (mt) cc_final: 0.8954 (mt) REVERT: B 655 THR cc_start: 0.9275 (t) cc_final: 0.9039 (t) REVERT: C 157 MET cc_start: 0.8352 (mtm) cc_final: 0.7960 (mtm) REVERT: C 177 TYR cc_start: 0.8973 (t80) cc_final: 0.8769 (t80) REVERT: C 200 ILE cc_start: 0.8405 (pt) cc_final: 0.8166 (pt) REVERT: C 212 ILE cc_start: 0.6382 (mt) cc_final: 0.5979 (mt) REVERT: C 237 GLU cc_start: 0.9332 (pm20) cc_final: 0.9116 (mm-30) REVERT: D 82 ASP cc_start: 0.8973 (m-30) cc_final: 0.8668 (p0) REVERT: D 137 MET cc_start: 0.6741 (ttt) cc_final: 0.6459 (tmm) REVERT: D 242 TYR cc_start: 0.9112 (t80) cc_final: 0.8759 (t80) REVERT: D 262 TYR cc_start: 0.8784 (t80) cc_final: 0.8543 (t80) REVERT: E 25 TRP cc_start: 0.8451 (p-90) cc_final: 0.8141 (p-90) outliers start: 1 outliers final: 1 residues processed: 593 average time/residue: 0.1234 time to fit residues: 112.6146 Evaluate side-chains 507 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 506 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 10.0000 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 390 GLN A 474 GLN B 447 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104814 restraints weight = 45708.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108995 restraints weight = 27553.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111702 restraints weight = 18495.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113529 restraints weight = 13680.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114790 restraints weight = 10865.647| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17041 Z= 0.152 Angle : 0.622 8.383 23026 Z= 0.325 Chirality : 0.043 0.183 2464 Planarity : 0.003 0.041 2931 Dihedral : 8.071 133.213 2373 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.82 (0.19), residues: 2012 helix: 1.08 (0.15), residues: 1173 sheet: -0.42 (0.40), residues: 175 loop : 0.05 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 350 TYR 0.016 0.002 TYR D 242 PHE 0.029 0.002 PHE A 81 TRP 0.008 0.001 TRP D 30 HIS 0.003 0.001 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17038) covalent geometry : angle 0.61804 / 0.32 (23020) SS BOND : bond 0.00729 / 0.37 ( 3) SS BOND : angle 4.50607 / 2.20 ( 6) hydrogen bonds : bond 0.03878 / 2.46 ( 912) hydrogen bonds : angle 4.93332 / 3.44 ( 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 603 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 0.622 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 65 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 147 GLN cc_start: 0.9014 (mt0) cc_final: 0.8622 (mt0) REVERT: A 161 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7493 (ptm160) REVERT: A 186 ILE cc_start: 0.9524 (mm) cc_final: 0.9293 (mm) REVERT: A 188 ILE cc_start: 0.9583 (mt) cc_final: 0.9364 (mt) REVERT: A 190 MET cc_start: 0.9317 (mtm) cc_final: 0.8999 (mtm) REVERT: A 250 TYR cc_start: 0.7375 (m-80) cc_final: 0.6928 (m-80) REVERT: A 255 HIS cc_start: 0.8001 (t-90) cc_final: 0.7530 (t70) REVERT: A 257 ASP cc_start: 0.8546 (m-30) cc_final: 0.8050 (m-30) REVERT: A 263 ASP cc_start: 0.9121 (m-30) cc_final: 0.8756 (m-30) REVERT: A 290 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 291 LEU cc_start: 0.9652 (mp) cc_final: 0.9066 (mt) REVERT: A 301 PHE cc_start: 0.8665 (m-80) cc_final: 0.8389 (m-80) REVERT: A 312 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8195 (tp40) REVERT: A 316 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 393 SER cc_start: 0.9133 (t) cc_final: 0.8266 (t) REVERT: A 402 GLU cc_start: 0.8360 (mp0) cc_final: 0.7671 (mp0) REVERT: A 403 ILE cc_start: 0.8478 (mm) cc_final: 0.8248 (mm) REVERT: A 447 ASN cc_start: 0.8830 (m-40) cc_final: 0.8518 (m-40) REVERT: A 501 GLN cc_start: 0.9448 (tt0) cc_final: 0.9076 (tm-30) REVERT: A 510 LYS cc_start: 0.8976 (tmtt) cc_final: 0.7547 (ttpt) REVERT: A 586 TYR cc_start: 0.9111 (m-80) cc_final: 0.8421 (m-80) REVERT: A 628 GLU cc_start: 0.9238 (tt0) cc_final: 0.8897 (tt0) REVERT: A 650 GLN cc_start: 0.8551 (mt0) cc_final: 0.8206 (mt0) REVERT: A 662 MET cc_start: 0.9064 (pmm) cc_final: 0.8557 (pmm) REVERT: A 664 THR cc_start: 0.9455 (p) cc_final: 0.9055 (p) REVERT: A 667 LEU cc_start: 0.9318 (tt) cc_final: 0.9107 (tt) REVERT: A 668 ASN cc_start: 0.9026 (m-40) cc_final: 0.8819 (m-40) REVERT: A 686 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7613 (mmm160) REVERT: B 40 TYR cc_start: 0.9211 (t80) cc_final: 0.8930 (t80) REVERT: B 99 LYS cc_start: 0.9448 (tptm) cc_final: 0.8914 (tptm) REVERT: B 118 TYR cc_start: 0.8983 (t80) cc_final: 0.8763 (t80) REVERT: B 119 GLU cc_start: 0.9423 (pm20) cc_final: 0.8987 (pm20) REVERT: B 120 ASP cc_start: 0.9304 (m-30) cc_final: 0.9077 (m-30) REVERT: B 150 GLN cc_start: 0.9290 (tp40) cc_final: 0.9022 (tp40) REVERT: B 158 ASN cc_start: 0.9053 (m-40) cc_final: 0.8460 (p0) REVERT: B 174 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7896 (tp30) REVERT: B 227 MET cc_start: 0.9175 (ptp) cc_final: 0.8651 (ptp) REVERT: B 235 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8392 (mtm-85) REVERT: B 335 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 349 LEU cc_start: 0.9572 (mt) cc_final: 0.9353 (mt) REVERT: B 375 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8167 (mmmm) REVERT: B 399 GLU cc_start: 0.8921 (tp30) cc_final: 0.8384 (tp30) REVERT: B 403 ILE cc_start: 0.9169 (mm) cc_final: 0.8843 (mm) REVERT: B 426 GLU cc_start: 0.8599 (pm20) cc_final: 0.8355 (pm20) REVERT: B 456 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8542 (mmtm) REVERT: B 471 TYR cc_start: 0.9219 (t80) cc_final: 0.8994 (t80) REVERT: B 496 ASN cc_start: 0.9399 (t0) cc_final: 0.9102 (t0) REVERT: B 575 ARG cc_start: 0.8709 (ptp90) cc_final: 0.8386 (ptp-170) REVERT: B 576 LEU cc_start: 0.9267 (mt) cc_final: 0.9066 (mt) REVERT: B 586 TYR cc_start: 0.9489 (m-80) cc_final: 0.9185 (m-80) REVERT: B 598 MET cc_start: 0.8707 (ttm) cc_final: 0.8356 (ttm) REVERT: B 599 GLU cc_start: 0.8559 (pp20) cc_final: 0.8020 (pp20) REVERT: B 602 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 604 ARG cc_start: 0.9425 (mmp80) cc_final: 0.9150 (mmp80) REVERT: B 627 LYS cc_start: 0.9035 (pttp) cc_final: 0.8628 (pttp) REVERT: B 632 MET cc_start: 0.8392 (mpp) cc_final: 0.8178 (mpp) REVERT: B 645 GLN cc_start: 0.9253 (tp40) cc_final: 0.8856 (tp40) REVERT: B 650 GLN cc_start: 0.6620 (mt0) cc_final: 0.6025 (mt0) REVERT: B 686 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6904 (tpt90) REVERT: C 157 MET cc_start: 0.8046 (mtm) cc_final: 0.7652 (mtm) REVERT: C 177 TYR cc_start: 0.8972 (t80) cc_final: 0.8667 (t80) REVERT: C 200 ILE cc_start: 0.8407 (pt) cc_final: 0.8199 (pt) REVERT: C 276 TYR cc_start: 0.8312 (t80) cc_final: 0.7948 (t80) REVERT: D 82 ASP cc_start: 0.8978 (m-30) cc_final: 0.8692 (p0) REVERT: D 137 MET cc_start: 0.6738 (ttt) cc_final: 0.6468 (ppp) REVERT: D 242 TYR cc_start: 0.9095 (t80) cc_final: 0.8799 (t80) REVERT: D 262 TYR cc_start: 0.8894 (t80) cc_final: 0.8658 (t80) REVERT: E 25 TRP cc_start: 0.8366 (p-90) cc_final: 0.8026 (p-90) REVERT: E 97 GLN cc_start: 0.8843 (mt0) cc_final: 0.8642 (mp10) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.1300 time to fit residues: 119.5023 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 : 0.651 ------------------------------------------------------------------------------- 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: 0.0020 chunk 25 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 467 ASN C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 201 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.151955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107285 restraints weight = 45492.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111315 restraints weight = 27832.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114033 restraints weight = 18652.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115687 restraints weight = 13857.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116906 restraints weight = 11107.964| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (20 function evaluations) r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17041 Z= 0.140 Angle : 0.636 9.007 23026 Z= 0.332 Chirality : 0.043 0.198 2464 Planarity : 0.003 0.040 2931 Dihedral : 7.912 136.028 2373 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.11 % 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: 0.72 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1167 sheet: -0.54 (0.39), residues: 179 loop : -0.05 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 350 TYR 0.026 0.001 TYR D 174 PHE 0.019 0.002 PHE A 492 TRP 0.009 0.001 TRP D 30 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (17038) covalent geometry : angle 0.63190 / 0.33 (23020) SS BOND : bond 0.00754 / 0.37 ( 3) SS BOND : angle 4.32979 / 2.07 ( 6) hydrogen bonds : bond 0.03866 / 2.47 ( 912) hydrogen bonds : angle 4.93928 / 3.45 ( 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 608 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 607 time to evaluate : 0.661 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: A 119 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 147 GLN cc_start: 0.9017 (mt0) cc_final: 0.8144 (mt0) REVERT: A 186 ILE cc_start: 0.9545 (mm) cc_final: 0.9335 (mm) REVERT: A 190 MET cc_start: 0.9331 (mtm) cc_final: 0.9031 (mtm) REVERT: A 250 TYR cc_start: 0.7395 (m-80) cc_final: 0.6918 (m-80) REVERT: A 255 HIS cc_start: 0.8407 (t-90) cc_final: 0.7935 (t70) REVERT: A 257 ASP cc_start: 0.8721 (m-30) cc_final: 0.8235 (m-30) REVERT: A 263 ASP cc_start: 0.9135 (m-30) cc_final: 0.8774 (m-30) REVERT: A 290 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 291 LEU cc_start: 0.9543 (mp) cc_final: 0.9001 (mp) REVERT: A 301 PHE cc_start: 0.8816 (m-80) cc_final: 0.8421 (m-80) REVERT: A 312 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7718 (tp40) REVERT: A 316 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 317 MET cc_start: 0.9048 (mmm) cc_final: 0.8836 (mmm) REVERT: A 322 MET cc_start: 0.8862 (mmm) cc_final: 0.8597 (mmm) REVERT: A 366 LYS cc_start: 0.9044 (ptpp) cc_final: 0.8821 (ptpp) REVERT: A 375 LYS cc_start: 0.8704 (mmtm) cc_final: 0.7987 (mmtm) REVERT: A 393 SER cc_start: 0.9100 (t) cc_final: 0.8230 (t) REVERT: A 402 GLU cc_start: 0.8408 (mp0) cc_final: 0.7725 (mp0) REVERT: A 447 ASN cc_start: 0.8800 (m-40) cc_final: 0.8500 (m-40) REVERT: A 456 LYS cc_start: 0.9076 (mppt) cc_final: 0.8849 (mppt) REVERT: A 501 GLN cc_start: 0.9457 (tt0) cc_final: 0.9057 (tm-30) REVERT: A 586 TYR cc_start: 0.9122 (m-80) cc_final: 0.8554 (m-80) REVERT: A 588 GLN cc_start: 0.8786 (tp40) cc_final: 0.8239 (tp40) REVERT: A 628 GLU cc_start: 0.9221 (tt0) cc_final: 0.8889 (tm-30) REVERT: A 650 GLN cc_start: 0.8416 (mt0) cc_final: 0.7917 (mt0) REVERT: A 664 THR cc_start: 0.9410 (p) cc_final: 0.9030 (p) REVERT: A 667 LEU cc_start: 0.9308 (tt) cc_final: 0.9106 (tt) REVERT: A 686 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7522 (mmm160) REVERT: B 40 TYR cc_start: 0.9184 (t80) cc_final: 0.8882 (t80) REVERT: B 99 LYS cc_start: 0.9525 (tptm) cc_final: 0.8914 (tptm) REVERT: B 119 GLU cc_start: 0.9445 (pm20) cc_final: 0.9032 (pm20) REVERT: B 120 ASP cc_start: 0.9260 (m-30) cc_final: 0.9040 (m-30) REVERT: B 150 GLN cc_start: 0.9266 (tp40) cc_final: 0.8970 (tp40) REVERT: B 158 ASN cc_start: 0.9014 (m-40) cc_final: 0.8484 (p0) REVERT: B 174 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7825 (tp30) REVERT: B 227 MET cc_start: 0.9179 (ptp) cc_final: 0.8620 (ptp) REVERT: B 235 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: B 274 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8119 (mmm160) REVERT: B 322 MET cc_start: 0.8603 (mmm) cc_final: 0.8359 (mmm) REVERT: B 335 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 344 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 348 MET cc_start: 0.8486 (tpt) cc_final: 0.8060 (tpp) REVERT: B 349 LEU cc_start: 0.9567 (mt) cc_final: 0.9363 (mt) REVERT: B 352 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6894 (mm-30) REVERT: B 375 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8159 (mmmm) REVERT: B 399 GLU cc_start: 0.8869 (tp30) cc_final: 0.8379 (tp30) REVERT: B 403 ILE cc_start: 0.9102 (mm) cc_final: 0.8770 (mm) REVERT: B 426 GLU cc_start: 0.8519 (pm20) cc_final: 0.8263 (pm20) REVERT: B 441 GLU cc_start: 0.9308 (pt0) cc_final: 0.9093 (pt0) REVERT: B 447 ASN cc_start: 0.8891 (m110) cc_final: 0.8586 (m-40) REVERT: B 456 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8492 (mmtm) REVERT: B 471 TYR cc_start: 0.9221 (t80) cc_final: 0.9002 (t80) REVERT: B 472 LEU cc_start: 0.9482 (mm) cc_final: 0.9266 (mt) REVERT: B 483 GLU cc_start: 0.9297 (pm20) cc_final: 0.9065 (pm20) REVERT: B 496 ASN cc_start: 0.9433 (t0) cc_final: 0.9142 (t0) REVERT: B 575 ARG cc_start: 0.8729 (ptp90) cc_final: 0.8413 (ptp-170) REVERT: B 586 TYR cc_start: 0.9484 (m-80) cc_final: 0.9206 (m-80) REVERT: B 598 MET cc_start: 0.8666 (ttm) cc_final: 0.8362 (ttm) REVERT: B 599 GLU cc_start: 0.8530 (pp20) cc_final: 0.8097 (pp20) REVERT: B 602 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 604 ARG cc_start: 0.9421 (mmp80) cc_final: 0.9140 (mmp80) REVERT: B 645 GLN cc_start: 0.9264 (tp40) cc_final: 0.8841 (tp40) REVERT: B 650 GLN cc_start: 0.6636 (mt0) cc_final: 0.6062 (mt0) REVERT: C 56 MET cc_start: 0.1691 (ptm) cc_final: 0.0970 (mmt) REVERT: C 177 TYR cc_start: 0.8928 (t80) cc_final: 0.8584 (t80) REVERT: C 200 ILE cc_start: 0.8314 (pt) cc_final: 0.8020 (pt) REVERT: D 82 ASP cc_start: 0.8948 (m-30) cc_final: 0.8696 (p0) REVERT: D 137 MET cc_start: 0.6742 (ttt) cc_final: 0.6521 (ppp) REVERT: D 242 TYR cc_start: 0.9089 (t80) cc_final: 0.8789 (t80) REVERT: D 262 TYR cc_start: 0.8884 (t80) cc_final: 0.8653 (t80) outliers start: 1 outliers final: 1 residues processed: 607 average time/residue: 0.1303 time to fit residues: 119.9346 Evaluate side-chains 513 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 645 GLN ** 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** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104652 restraints weight = 46214.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108807 restraints weight = 27770.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111561 restraints weight = 18446.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113375 restraints weight = 13678.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114610 restraints weight = 10812.075| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17041 Z= 0.171 Angle : 0.670 9.422 23026 Z= 0.350 Chirality : 0.044 0.185 2464 Planarity : 0.004 0.040 2931 Dihedral : 7.900 136.874 2373 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.59 (0.18), residues: 2012 helix: 0.94 (0.15), residues: 1167 sheet: -0.53 (0.40), residues: 177 loop : -0.12 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 350 TYR 0.024 0.002 TYR D 105 PHE 0.022 0.002 PHE C 227 TRP 0.013 0.001 TRP D 30 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17038) covalent geometry : angle 0.66607 / 0.35 (23020) SS BOND : bond 0.00419 / 0.21 ( 3) SS BOND : angle 4.47749 / 2.14 ( 6) hydrogen bonds : bond 0.03978 / 2.51 ( 912) hydrogen bonds : angle 5.03941 / 3.53 ( 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 589 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.659 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 147 GLN cc_start: 0.9066 (mt0) cc_final: 0.8634 (mt0) REVERT: A 186 ILE cc_start: 0.9558 (mm) cc_final: 0.9281 (mm) REVERT: A 188 ILE cc_start: 0.9563 (mt) cc_final: 0.9351 (mt) REVERT: A 190 MET cc_start: 0.9273 (mtm) cc_final: 0.8973 (mtm) REVERT: A 250 TYR cc_start: 0.7463 (m-80) cc_final: 0.7002 (m-80) REVERT: A 255 HIS cc_start: 0.8449 (t-90) cc_final: 0.8048 (t70) REVERT: A 257 ASP cc_start: 0.8719 (m-30) cc_final: 0.8319 (m-30) REVERT: A 263 ASP cc_start: 0.9122 (m-30) cc_final: 0.8737 (m-30) REVERT: A 290 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 291 LEU cc_start: 0.9549 (mp) cc_final: 0.8970 (mp) REVERT: A 301 PHE cc_start: 0.8799 (m-80) cc_final: 0.8424 (m-80) REVERT: A 312 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7844 (tp40) REVERT: A 316 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 322 MET cc_start: 0.8821 (mmm) cc_final: 0.8516 (mmm) REVERT: A 447 ASN cc_start: 0.8816 (m-40) cc_final: 0.8516 (m-40) REVERT: A 456 LYS cc_start: 0.9057 (mppt) cc_final: 0.8849 (mppt) REVERT: A 490 THR cc_start: 0.9045 (m) cc_final: 0.8059 (p) REVERT: A 494 MET cc_start: 0.8560 (mmp) cc_final: 0.8123 (mmp) REVERT: A 501 GLN cc_start: 0.9463 (tt0) cc_final: 0.9053 (tm-30) REVERT: A 586 TYR cc_start: 0.9137 (m-80) cc_final: 0.8608 (m-80) REVERT: A 628 GLU cc_start: 0.9232 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 650 GLN cc_start: 0.8411 (mt0) cc_final: 0.8011 (mt0) REVERT: A 686 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7604 (mmm160) REVERT: B 40 TYR cc_start: 0.9161 (t80) cc_final: 0.8852 (t80) REVERT: B 99 LYS cc_start: 0.9522 (tptm) cc_final: 0.8953 (tptp) REVERT: B 119 GLU cc_start: 0.9447 (pm20) cc_final: 0.9073 (pm20) REVERT: B 150 GLN cc_start: 0.9257 (tp40) cc_final: 0.8887 (tp40) REVERT: B 158 ASN cc_start: 0.8977 (m-40) cc_final: 0.8405 (p0) REVERT: B 174 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8249 (tp30) REVERT: B 227 MET cc_start: 0.9130 (ptp) cc_final: 0.8638 (ptp) REVERT: B 274 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8184 (mmm160) REVERT: B 314 MET cc_start: 0.8755 (ttp) cc_final: 0.8487 (ttp) REVERT: B 335 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 344 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 375 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8173 (mmmm) REVERT: B 390 GLN cc_start: 0.9276 (mt0) cc_final: 0.9040 (mm-40) REVERT: B 399 GLU cc_start: 0.8945 (tp30) cc_final: 0.8390 (tp30) REVERT: B 403 ILE cc_start: 0.9081 (mm) cc_final: 0.8810 (mm) REVERT: B 426 GLU cc_start: 0.8526 (pm20) cc_final: 0.8248 (pm20) REVERT: B 427 LYS cc_start: 0.9331 (mmpt) cc_final: 0.8973 (mmmt) REVERT: B 447 ASN cc_start: 0.8811 (m110) cc_final: 0.8439 (m-40) REVERT: B 466 MET cc_start: 0.8680 (ptt) cc_final: 0.8454 (ptt) REVERT: B 496 ASN cc_start: 0.9389 (t0) cc_final: 0.9118 (t0) REVERT: B 501 GLN cc_start: 0.9477 (tt0) cc_final: 0.9236 (tm-30) REVERT: B 575 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8239 (ptp-170) REVERT: B 598 MET cc_start: 0.8696 (ttm) cc_final: 0.8370 (ttm) REVERT: B 599 GLU cc_start: 0.8544 (pp20) cc_final: 0.8070 (pp20) REVERT: B 602 GLU cc_start: 0.8696 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 604 ARG cc_start: 0.9425 (mmp80) cc_final: 0.9095 (mmp80) REVERT: B 645 GLN cc_start: 0.9283 (tp40) cc_final: 0.8753 (tp40) REVERT: B 650 GLN cc_start: 0.6553 (mt0) cc_final: 0.5960 (mt0) REVERT: C 200 ILE cc_start: 0.8152 (pt) cc_final: 0.7878 (pt) REVERT: C 212 ILE cc_start: 0.7089 (mt) cc_final: 0.6640 (mt) REVERT: C 315 LEU cc_start: 0.8176 (mt) cc_final: 0.7931 (mt) REVERT: D 82 ASP cc_start: 0.8943 (m-30) cc_final: 0.8724 (p0) REVERT: D 137 MET cc_start: 0.6806 (ttt) cc_final: 0.6564 (tmm) REVERT: D 242 TYR cc_start: 0.9150 (t80) cc_final: 0.8847 (t80) REVERT: D 262 TYR cc_start: 0.8931 (t80) cc_final: 0.8706 (t80) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.1296 time to fit residues: 116.6823 Evaluate side-chains 487 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 0.3980 chunk 96 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 232 ASN A 467 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 320 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 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 = 0.4072 r_free = 0.4072 target = 0.153260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108984 restraints weight = 45838.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112961 restraints weight = 27743.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115650 restraints weight = 18606.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117386 restraints weight = 13859.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118631 restraints weight = 10988.993| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17041 Z= 0.142 Angle : 0.671 10.060 23026 Z= 0.353 Chirality : 0.045 0.184 2464 Planarity : 0.004 0.041 2931 Dihedral : 7.767 135.889 2373 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % 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: 0.55 (0.19), residues: 2012 helix: 0.87 (0.15), residues: 1171 sheet: -0.29 (0.41), residues: 173 loop : -0.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 350 TYR 0.019 0.001 TYR D 174 PHE 0.035 0.002 PHE C 92 TRP 0.016 0.001 TRP D 30 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17038) covalent geometry : angle 0.66614 / 0.35 (23020) SS BOND : bond 0.00918 / 0.44 ( 3) SS BOND : angle 4.90636 / 2.36 ( 6) hydrogen bonds : bond 0.03970 / 2.51 ( 912) hydrogen bonds : angle 5.04855 / 3.55 ( 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 612 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 611 time to evaluate : 0.623 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 147 GLN cc_start: 0.8980 (mt0) cc_final: 0.8063 (mt0) REVERT: A 157 LEU cc_start: 0.9179 (tp) cc_final: 0.8566 (tp) REVERT: A 164 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8214 (ttm110) REVERT: A 186 ILE cc_start: 0.9547 (mm) cc_final: 0.9288 (mm) REVERT: A 188 ILE cc_start: 0.9598 (mt) cc_final: 0.9257 (mt) REVERT: A 190 MET cc_start: 0.9316 (mtm) cc_final: 0.9019 (mtm) REVERT: A 250 TYR cc_start: 0.7438 (m-80) cc_final: 0.6920 (m-80) REVERT: A 255 HIS cc_start: 0.8528 (t-90) cc_final: 0.8120 (t70) REVERT: A 257 ASP cc_start: 0.8774 (m-30) cc_final: 0.8330 (m-30) REVERT: A 263 ASP cc_start: 0.9155 (m-30) cc_final: 0.8850 (m-30) REVERT: A 290 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 291 LEU cc_start: 0.9554 (mp) cc_final: 0.9058 (mt) REVERT: A 301 PHE cc_start: 0.8746 (m-80) cc_final: 0.8425 (m-80) REVERT: A 312 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7677 (tp40) REVERT: A 316 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 322 MET cc_start: 0.8868 (mmm) cc_final: 0.8515 (mmm) REVERT: A 375 LYS cc_start: 0.8687 (mmtm) cc_final: 0.7908 (mmtm) REVERT: A 447 ASN cc_start: 0.8852 (m-40) cc_final: 0.8206 (m-40) REVERT: A 456 LYS cc_start: 0.9075 (mppt) cc_final: 0.8851 (mppt) REVERT: A 490 THR cc_start: 0.9048 (m) cc_final: 0.8706 (p) REVERT: A 501 GLN cc_start: 0.9454 (tt0) cc_final: 0.9046 (tm-30) REVERT: A 510 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8907 (ttmm) REVERT: A 586 TYR cc_start: 0.9078 (m-80) cc_final: 0.8711 (m-80) REVERT: A 588 GLN cc_start: 0.8596 (tp40) cc_final: 0.8191 (tp40) REVERT: A 628 GLU cc_start: 0.9282 (tt0) cc_final: 0.8993 (tm-30) REVERT: A 650 GLN cc_start: 0.8389 (mt0) cc_final: 0.7799 (mt0) REVERT: A 667 LEU cc_start: 0.9402 (tt) cc_final: 0.9196 (tt) REVERT: A 686 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7469 (mmm160) REVERT: B 40 TYR cc_start: 0.9182 (t80) cc_final: 0.8898 (t80) REVERT: B 99 LYS cc_start: 0.9505 (tptm) cc_final: 0.8930 (tptp) REVERT: B 119 GLU cc_start: 0.9382 (pm20) cc_final: 0.8991 (pm20) REVERT: B 158 ASN cc_start: 0.8948 (m-40) cc_final: 0.8401 (p0) REVERT: B 174 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8039 (tp30) REVERT: B 227 MET cc_start: 0.9167 (ptp) cc_final: 0.8594 (ptp) REVERT: B 235 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8023 (mtm-85) REVERT: B 274 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8211 (mmm160) REVERT: B 335 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8043 (mt-10) REVERT: B 344 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 348 MET cc_start: 0.8408 (tpt) cc_final: 0.8194 (tpp) REVERT: B 349 LEU cc_start: 0.9544 (mt) cc_final: 0.9334 (mt) REVERT: B 375 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8177 (mmmm) REVERT: B 390 GLN cc_start: 0.9218 (mt0) cc_final: 0.8987 (mm-40) REVERT: B 399 GLU cc_start: 0.8934 (tp30) cc_final: 0.8431 (tp30) REVERT: B 403 ILE cc_start: 0.9012 (mm) cc_final: 0.8439 (tp) REVERT: B 426 GLU cc_start: 0.8553 (pm20) cc_final: 0.8128 (pm20) REVERT: B 427 LYS cc_start: 0.9323 (mmpt) cc_final: 0.8906 (mmmt) REVERT: B 447 ASN cc_start: 0.8751 (m110) cc_final: 0.8529 (m-40) REVERT: B 456 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8516 (mmtm) REVERT: B 483 GLU cc_start: 0.9307 (pm20) cc_final: 0.8850 (pm20) REVERT: B 496 ASN cc_start: 0.9403 (t0) cc_final: 0.9045 (t0) REVERT: B 500 ILE cc_start: 0.9697 (mt) cc_final: 0.9414 (mt) REVERT: B 501 GLN cc_start: 0.9466 (tt0) cc_final: 0.9187 (tm-30) REVERT: B 570 MET cc_start: 0.8895 (tpp) cc_final: 0.8559 (tpp) REVERT: B 575 ARG cc_start: 0.8729 (ptp90) cc_final: 0.8512 (ptp-170) REVERT: B 576 LEU cc_start: 0.9232 (mt) cc_final: 0.9009 (mt) REVERT: B 598 MET cc_start: 0.8589 (ttm) cc_final: 0.8310 (ttm) REVERT: B 599 GLU cc_start: 0.8624 (pp20) cc_final: 0.8252 (pp20) REVERT: B 602 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 604 ARG cc_start: 0.9430 (mmp80) cc_final: 0.9079 (mmp80) REVERT: B 645 GLN cc_start: 0.9279 (tp40) cc_final: 0.8782 (tp40) REVERT: B 650 GLN cc_start: 0.6566 (mt0) cc_final: 0.5992 (mt0) REVERT: B 652 ILE cc_start: 0.9350 (mt) cc_final: 0.9122 (mt) REVERT: B 673 TYR cc_start: 0.8825 (t80) cc_final: 0.8614 (t80) REVERT: B 677 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.7987 (mmm-85) REVERT: C 200 ILE cc_start: 0.8353 (pt) cc_final: 0.8085 (pt) REVERT: D 242 TYR cc_start: 0.9123 (t80) cc_final: 0.8772 (t80) REVERT: D 262 TYR cc_start: 0.8924 (t80) cc_final: 0.8714 (t80) outliers start: 1 outliers final: 1 residues processed: 611 average time/residue: 0.1272 time to fit residues: 118.2802 Evaluate side-chains 513 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** 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** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106011 restraints weight = 46215.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110085 restraints weight = 28092.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112830 restraints weight = 18978.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114586 restraints weight = 14054.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115842 restraints weight = 11240.421| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17041 Z= 0.162 Angle : 0.675 10.877 23026 Z= 0.357 Chirality : 0.045 0.212 2464 Planarity : 0.004 0.040 2931 Dihedral : 7.739 136.690 2373 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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 (0.19), residues: 2012 helix: 0.81 (0.15), residues: 1171 sheet: -0.28 (0.41), residues: 169 loop : -0.20 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 502 TYR 0.019 0.002 TYR D 105 PHE 0.024 0.002 PHE C 92 TRP 0.016 0.001 TRP D 30 HIS 0.009 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (17038) covalent geometry : angle 0.66968 / 0.35 (23020) SS BOND : bond 0.00827 / 0.41 ( 3) SS BOND : angle 5.14001 / 2.45 ( 6) hydrogen bonds : bond 0.03948 / 2.51 ( 912) hydrogen bonds : angle 5.11554 / 3.58 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.53 seconds wall clock time: 64 minutes 57.96 seconds (3897.96 seconds total)