Starting phenix.real_space_refine on Thu Aug 6 17:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxs_45010/08_2026/9bxs_45010.cif" } resolution = 3.37 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 2.91, per 1000 atoms: 0.17 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 136.89, 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: 1.15 Conformation dependent library (CDL) restraints added in 722.8 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: 0.43 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: 3.770A 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: 4.066A 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: 3.662A 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: 3.567A 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: 4.059A 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: 4.045A 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: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.234A 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: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A 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: 4.256A 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: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A 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: 3.567A 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: 4.874A 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: 3.527A 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: 6.234A 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: 7.540A 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: 6.485A 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: 6.479A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A 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: 6.587A 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: 6.147A 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: 5.385A 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: 2.92 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4866 1.33 - 1.46: 3195 1.46 - 1.58: 8788 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 1.608 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " ideal model delta sigma weight residual 1.748 1.612 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP B 802 " pdb=" PB TTP B 802 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.17e+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 1.15e+01 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22191 2.09 - 4.19: 723 4.19 - 6.28: 85 6.28 - 8.38: 13 8.38 - 10.47: 8 Bond angle restraints: 23020 Sorted by residual: angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.35 5.85 1.30e+00 5.92e-01 2.03e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.66 -6.12 1.36e+00 5.41e-01 2.02e+01 angle pdb=" OE1 GLN E 44 " pdb=" CD GLN E 44 " pdb=" NE2 GLN E 44 " ideal model delta sigma weight residual 122.60 118.53 4.07 1.00e+00 1.00e+00 1.66e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.45 -4.26 1.06e+00 8.90e-01 1.62e+01 angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 113.71 109.96 3.75 9.50e-01 1.11e+00 1.56e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.13: 9481 26.13 - 52.27: 702 52.27 - 78.40: 105 78.40 - 104.54: 14 104.54 - 130.67: 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 -170.24 84.24 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 -103.65 130.67 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 -101.14 128.16 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: 2214 0.093 - 0.186: 213 0.186 - 0.278: 32 0.278 - 0.371: 3 0.371 - 0.464: 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 2.05 0.46 2.00e-01 2.50e+01 5.38e+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 4.68e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.69e-02 3.40e+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 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.007 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 " -0.014 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 " 0.046 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP B 623 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 624 " 0.038 2.00e-02 2.50e+03 2.37e-02 9.79e+00 pdb=" CG PHE B 624 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 624 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 624 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 624 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 624 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 624 " 0.023 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 123 2.51 - 3.11: 11991 3.11 - 3.70: 27803 3.70 - 4.30: 42500 4.30 - 4.90: 68512 Nonbonded interactions: 150929 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150924 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.010 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 0.629 17041 Z= 0.432 Angle : 0.867 13.507 23026 Z= 0.522 Chirality : 0.059 0.464 2464 Planarity : 0.004 0.041 2931 Dihedral : 17.523 130.674 6447 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.34 % Allowed : 16.32 % 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: 0.58 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.32 (0.37), residues: 179 loop : 0.45 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.039 0.002 TYR E 67 PHE 0.038 0.003 PHE B 624 TRP 0.077 0.006 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.36 (17038) covalent geometry : angle 0.86146 / 0.52 (23020) SS BOND : bond 0.36318 / 13.45 ( 3) SS BOND : angle 6.07804 / 3.50 ( 6) hydrogen bonds : bond 0.16748 / 11.21 ( 912) hydrogen bonds : angle 6.70611 / 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 651 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 627 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8555 (mmtt) REVERT: A 263 ASP cc_start: 0.8059 (m-30) cc_final: 0.7733 (m-30) REVERT: A 286 ASP cc_start: 0.7667 (m-30) cc_final: 0.7369 (m-30) REVERT: A 362 ASP cc_start: 0.7358 (m-30) cc_final: 0.7043 (m-30) REVERT: A 441 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7156 (mt-10) REVERT: A 604 ARG cc_start: 0.8173 (mmp80) cc_final: 0.7670 (mmp80) REVERT: A 606 TYR cc_start: 0.7135 (m-80) cc_final: 0.6860 (m-10) REVERT: A 632 MET cc_start: 0.8539 (mtt) cc_final: 0.8230 (mtt) REVERT: B 106 LEU cc_start: 0.8744 (tp) cc_final: 0.8536 (tp) REVERT: B 177 ASP cc_start: 0.8434 (t0) cc_final: 0.8206 (t0) REVERT: B 315 ASP cc_start: 0.8448 (p0) cc_final: 0.8199 (p0) REVERT: B 322 MET cc_start: 0.8617 (mmm) cc_final: 0.8413 (mmt) REVERT: B 385 VAL cc_start: 0.8981 (t) cc_final: 0.8570 (t) REVERT: B 586 TYR cc_start: 0.8195 (m-80) cc_final: 0.7892 (m-80) REVERT: B 598 MET cc_start: 0.7634 (mtp) cc_final: 0.7356 (mtp) REVERT: C 137 MET cc_start: 0.3070 (mtp) cc_final: 0.2711 (mtp) outliers start: 24 outliers final: 5 residues processed: 644 average time/residue: 0.1202 time to fit residues: 115.9105 Evaluate side-chains 426 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 420 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN A 329 ASN B 14 ASN B 34 HIS B 180 ASN B 232 ASN B 320 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN D 69 GLN D 80 HIS D 132 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.184134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101621 restraints weight = 25938.975| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.20 r_work: 0.2915 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17041 Z= 0.266 Angle : 0.658 18.045 23026 Z= 0.344 Chirality : 0.045 0.169 2464 Planarity : 0.004 0.042 2931 Dihedral : 9.250 136.311 2389 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.02 % Allowed : 17.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2012 helix: 1.50 (0.15), residues: 1166 sheet: -0.06 (0.41), residues: 153 loop : 0.45 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.019 0.002 TYR C 169 PHE 0.019 0.002 PHE B 492 TRP 0.021 0.002 TRP A 558 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.27 (17038) covalent geometry : angle 0.65679 / 0.34 (23020) SS BOND : bond 0.00370 / 0.16 ( 3) SS BOND : angle 2.79451 / 1.53 ( 6) hydrogen bonds : bond 0.04632 / 3.00 ( 912) hydrogen bonds : angle 4.92593 / 3.38 ( 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 480 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 426 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8820 (mmmm) REVERT: A 29 ASP cc_start: 0.9346 (t0) cc_final: 0.8955 (t70) REVERT: A 49 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8761 (t-90) REVERT: A 65 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8008 (mp0) REVERT: A 191 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8951 (mm-40) REVERT: A 209 LYS cc_start: 0.9286 (ttpp) cc_final: 0.9078 (ttmm) REVERT: A 217 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8909 (mm-30) REVERT: A 250 TYR cc_start: 0.9311 (m-80) cc_final: 0.8779 (m-80) REVERT: A 263 ASP cc_start: 0.8908 (m-30) cc_final: 0.8397 (m-30) REVERT: A 286 ASP cc_start: 0.8897 (m-30) cc_final: 0.8257 (m-30) REVERT: A 352 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8729 (mt-10) REVERT: A 362 ASP cc_start: 0.8504 (m-30) cc_final: 0.7984 (m-30) REVERT: A 379 SER cc_start: 0.9438 (t) cc_final: 0.9032 (t) REVERT: A 586 TYR cc_start: 0.9332 (m-80) cc_final: 0.9072 (m-80) REVERT: B 11 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8869 (pt0) REVERT: B 65 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8399 (mm-30) REVERT: B 104 TYR cc_start: 0.9229 (m-80) cc_final: 0.8759 (m-80) REVERT: B 138 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9233 (mtmm) REVERT: B 148 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8603 (mt-10) REVERT: B 150 GLN cc_start: 0.9234 (tp40) cc_final: 0.8696 (tp-100) REVERT: B 177 ASP cc_start: 0.8860 (t0) cc_final: 0.8606 (t70) REVERT: B 238 ASP cc_start: 0.8206 (p0) cc_final: 0.7943 (t0) REVERT: B 243 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5429 (ttt180) REVERT: B 266 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8374 (mtpp) REVERT: B 274 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8412 (ttm-80) REVERT: B 296 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8411 (mmmt) REVERT: B 321 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 333 LYS cc_start: 0.9395 (tttt) cc_final: 0.9043 (mtpp) REVERT: B 493 MET cc_start: 0.9639 (tmm) cc_final: 0.9355 (tmm) REVERT: B 515 ASP cc_start: 0.9125 (m-30) cc_final: 0.8704 (m-30) REVERT: B 586 TYR cc_start: 0.9242 (m-80) cc_final: 0.8784 (m-80) REVERT: B 588 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8545 (mm-40) REVERT: B 602 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8101 (tt0) REVERT: B 615 MET cc_start: 0.9540 (mmp) cc_final: 0.9247 (mmp) REVERT: B 630 TYR cc_start: 0.9149 (m-80) cc_final: 0.8901 (m-80) REVERT: B 659 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8634 (mtpp) REVERT: B 662 MET cc_start: 0.8503 (ptp) cc_final: 0.8247 (ptp) REVERT: B 686 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8213 (mtp85) REVERT: C 95 MET cc_start: 0.0780 (ppp) cc_final: 0.0458 (ppp) REVERT: C 130 TYR cc_start: 0.6733 (m-80) cc_final: 0.6463 (m-10) REVERT: C 137 MET cc_start: -0.0145 (mtp) cc_final: -0.0371 (mtp) REVERT: C 155 LYS cc_start: 0.4089 (mmtp) cc_final: 0.3549 (ptmt) REVERT: D 91 ASN cc_start: 0.2463 (m-40) cc_final: 0.1862 (t0) REVERT: D 185 MET cc_start: 0.7254 (mmm) cc_final: 0.6953 (mmm) REVERT: D 189 GLU cc_start: 0.5975 (tt0) cc_final: 0.5504 (pt0) REVERT: E 46 MET cc_start: 0.8624 (tpt) cc_final: 0.8326 (tpt) outliers start: 54 outliers final: 21 residues processed: 460 average time/residue: 0.1185 time to fit residues: 81.5483 Evaluate side-chains 403 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 376 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 38 VAL 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: 0.9980 chunk 138 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 chunk 130 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 146 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 475 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** E 60 ASN ** 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 = 0.4209 r_free = 0.4209 target = 0.189419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110692 restraints weight = 26277.742| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.48 r_work: 0.2977 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17041 Z= 0.144 Angle : 0.558 14.767 23026 Z= 0.291 Chirality : 0.042 0.173 2464 Planarity : 0.003 0.043 2931 Dihedral : 8.622 133.604 2379 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.91 % Allowed : 17.10 % Favored : 79.99 % 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: 1.58 (0.19), residues: 2012 helix: 1.65 (0.15), residues: 1168 sheet: 0.00 (0.42), residues: 153 loop : 0.43 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 686 TYR 0.020 0.001 TYR C 22 PHE 0.018 0.001 PHE A 492 TRP 0.011 0.001 TRP A 558 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17038) covalent geometry : angle 0.55675 / 0.29 (23020) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 2.12569 / 1.15 ( 6) hydrogen bonds : bond 0.03986 / 2.57 ( 912) hydrogen bonds : angle 4.69167 / 3.22 ( 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 470 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 418 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8821 (mmmm) REVERT: A 29 ASP cc_start: 0.9313 (t0) cc_final: 0.8909 (t70) REVERT: A 49 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8731 (t-90) REVERT: A 65 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7658 (mp0) REVERT: A 136 LYS cc_start: 0.9279 (tptt) cc_final: 0.8954 (tptp) REVERT: A 144 MET cc_start: 0.9346 (mtm) cc_final: 0.9128 (mtp) REVERT: A 209 LYS cc_start: 0.9224 (ttpp) cc_final: 0.9022 (ttmm) REVERT: A 217 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8925 (mm-30) REVERT: A 231 ASP cc_start: 0.9349 (t0) cc_final: 0.9065 (t0) REVERT: A 250 TYR cc_start: 0.9321 (m-80) cc_final: 0.8857 (m-80) REVERT: A 263 ASP cc_start: 0.8792 (m-30) cc_final: 0.8337 (m-30) REVERT: A 276 LYS cc_start: 0.9219 (mmtp) cc_final: 0.9014 (mmtp) REVERT: A 286 ASP cc_start: 0.8877 (m-30) cc_final: 0.8203 (m-30) REVERT: A 290 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 352 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8706 (mt-10) REVERT: A 362 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: A 379 SER cc_start: 0.9402 (t) cc_final: 0.9051 (t) REVERT: A 385 VAL cc_start: 0.9420 (t) cc_final: 0.9198 (p) REVERT: A 602 GLU cc_start: 0.8644 (tt0) cc_final: 0.7872 (tt0) REVERT: A 604 ARG cc_start: 0.8832 (mmp80) cc_final: 0.8563 (mmp80) REVERT: A 639 ASP cc_start: 0.9207 (m-30) cc_final: 0.8941 (m-30) REVERT: B 15 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 65 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8317 (mm-30) REVERT: B 104 TYR cc_start: 0.9114 (m-80) cc_final: 0.8720 (m-80) REVERT: B 106 LEU cc_start: 0.9310 (tp) cc_final: 0.9070 (tp) REVERT: B 296 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8261 (mmmt) REVERT: B 333 LYS cc_start: 0.9378 (tttt) cc_final: 0.9177 (mtpp) REVERT: B 475 ASN cc_start: 0.9431 (m110) cc_final: 0.9088 (m-40) REVERT: B 493 MET cc_start: 0.9628 (tmm) cc_final: 0.9321 (tmm) REVERT: B 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8672 (m-30) REVERT: B 586 TYR cc_start: 0.9201 (m-80) cc_final: 0.8778 (m-80) REVERT: B 602 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8025 (tt0) REVERT: B 662 MET cc_start: 0.8505 (ptp) cc_final: 0.8279 (ptp) REVERT: B 684 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: B 686 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8187 (mtp85) REVERT: C 130 TYR cc_start: 0.6867 (m-80) cc_final: 0.6598 (m-10) REVERT: C 137 MET cc_start: -0.0085 (mtp) cc_final: -0.0322 (mtp) REVERT: C 155 LYS cc_start: 0.4170 (mmtp) cc_final: 0.3674 (ptmt) REVERT: D 91 ASN cc_start: 0.2533 (m-40) cc_final: 0.1956 (t0) REVERT: D 269 MET cc_start: 0.3714 (tpt) cc_final: 0.3148 (mpp) REVERT: E 46 MET cc_start: 0.8749 (tpt) cc_final: 0.8355 (tpt) outliers start: 52 outliers final: 26 residues processed: 449 average time/residue: 0.1252 time to fit residues: 84.6930 Evaluate side-chains 418 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 388 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 165 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 218 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105896 restraints weight = 26464.035| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.17 r_work: 0.2933 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17041 Z= 0.164 Angle : 0.555 13.906 23026 Z= 0.290 Chirality : 0.042 0.170 2464 Planarity : 0.003 0.043 2931 Dihedral : 8.347 135.894 2375 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.02 % Allowed : 17.55 % Favored : 79.43 % 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: 1.63 (0.19), residues: 2012 helix: 1.71 (0.15), residues: 1172 sheet: -0.08 (0.42), residues: 153 loop : 0.42 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 686 TYR 0.026 0.002 TYR D 105 PHE 0.018 0.001 PHE C 259 TRP 0.008 0.001 TRP A 558 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17038) covalent geometry : angle 0.55313 / 0.29 (23020) SS BOND : bond 0.00303 / 0.16 ( 3) SS BOND : angle 2.71855 / 1.47 ( 6) hydrogen bonds : bond 0.03786 / 2.42 ( 912) hydrogen bonds : angle 4.64067 / 3.18 ( 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 453 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8826 (mmmm) REVERT: A 30 LYS cc_start: 0.8906 (tptp) cc_final: 0.8608 (tptt) REVERT: A 49 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8842 (t-90) REVERT: A 65 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7621 (mp0) REVERT: A 136 LYS cc_start: 0.9237 (tptt) cc_final: 0.8894 (tptp) REVERT: A 144 MET cc_start: 0.9411 (mtm) cc_final: 0.9176 (mtp) REVERT: A 217 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8900 (mm-30) REVERT: A 250 TYR cc_start: 0.9349 (m-80) cc_final: 0.8779 (m-80) REVERT: A 263 ASP cc_start: 0.8791 (m-30) cc_final: 0.8401 (m-30) REVERT: A 286 ASP cc_start: 0.8913 (m-30) cc_final: 0.8184 (m-30) REVERT: A 290 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 352 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8681 (mt-10) REVERT: A 362 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: A 379 SER cc_start: 0.9423 (t) cc_final: 0.9030 (t) REVERT: A 420 MET cc_start: 0.9551 (mmm) cc_final: 0.9349 (mmm) REVERT: A 458 MET cc_start: 0.9102 (mmm) cc_final: 0.8840 (mmt) REVERT: A 570 MET cc_start: 0.8932 (mtp) cc_final: 0.8727 (mtp) REVERT: A 602 GLU cc_start: 0.8670 (tt0) cc_final: 0.7680 (tt0) REVERT: A 604 ARG cc_start: 0.8681 (mmp80) cc_final: 0.8396 (mmp80) REVERT: B 15 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8515 (mm-30) REVERT: B 21 ASP cc_start: 0.9147 (t0) cc_final: 0.8668 (t0) REVERT: B 65 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8345 (mm-30) REVERT: B 66 GLU cc_start: 0.8525 (tp30) cc_final: 0.8278 (tp30) REVERT: B 104 TYR cc_start: 0.9221 (m-80) cc_final: 0.8946 (m-80) REVERT: B 144 MET cc_start: 0.9376 (mtm) cc_final: 0.8869 (mtp) REVERT: B 148 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8544 (mt-10) REVERT: B 266 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8756 (mtpp) REVERT: B 296 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8380 (mmmt) REVERT: B 402 GLU cc_start: 0.8877 (mp0) cc_final: 0.8510 (mp0) REVERT: B 471 TYR cc_start: 0.9381 (t80) cc_final: 0.9051 (t80) REVERT: B 475 ASN cc_start: 0.9466 (m110) cc_final: 0.8985 (m-40) REVERT: B 493 MET cc_start: 0.9681 (tmm) cc_final: 0.9418 (tmm) REVERT: B 515 ASP cc_start: 0.9123 (m-30) cc_final: 0.8619 (m-30) REVERT: B 586 TYR cc_start: 0.9199 (m-80) cc_final: 0.8874 (m-80) REVERT: B 602 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8039 (tt0) REVERT: B 610 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8862 (mtmm) REVERT: B 612 TYR cc_start: 0.9303 (m-80) cc_final: 0.9084 (m-80) REVERT: B 684 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7442 (m-10) REVERT: B 686 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8104 (mtp85) REVERT: C 130 TYR cc_start: 0.6946 (m-80) cc_final: 0.6708 (m-10) REVERT: C 137 MET cc_start: 0.0034 (mtp) cc_final: -0.0183 (mtp) REVERT: C 155 LYS cc_start: 0.4351 (mmtp) cc_final: 0.3958 (ptmt) REVERT: D 74 MET cc_start: 0.0189 (ttm) cc_final: -0.0053 (tpt) REVERT: D 91 ASN cc_start: 0.2111 (m-40) cc_final: 0.1782 (t0) REVERT: D 269 MET cc_start: 0.3384 (tpt) cc_final: 0.2896 (mpp) REVERT: E 46 MET cc_start: 0.8626 (tpt) cc_final: 0.8194 (tpt) outliers start: 54 outliers final: 36 residues processed: 434 average time/residue: 0.1321 time to fit residues: 86.7975 Evaluate side-chains 409 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 172 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 265 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.188462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108427 restraints weight = 26596.794| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.30 r_work: 0.2920 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17041 Z= 0.177 Angle : 0.565 16.671 23026 Z= 0.293 Chirality : 0.042 0.204 2464 Planarity : 0.003 0.042 2931 Dihedral : 8.333 137.703 2375 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.91 % Allowed : 18.11 % Favored : 78.98 % 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: 1.58 (0.19), residues: 2012 helix: 1.72 (0.15), residues: 1178 sheet: -0.34 (0.41), residues: 157 loop : 0.35 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.018 0.001 TYR A 140 PHE 0.018 0.001 PHE C 92 TRP 0.008 0.001 TRP A 558 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (17038) covalent geometry : angle 0.56350 / 0.29 (23020) SS BOND : bond 0.00738 / 0.39 ( 3) SS BOND : angle 2.88266 / 1.52 ( 6) hydrogen bonds : bond 0.03681 / 2.34 ( 912) hydrogen bonds : angle 4.61334 / 3.17 ( 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 441 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 389 time to evaluate : 0.648 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: A 23 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8838 (mmmm) REVERT: A 30 LYS cc_start: 0.8860 (tptp) cc_final: 0.8612 (tptt) REVERT: A 49 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8857 (t-90) REVERT: A 65 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7802 (mp0) REVERT: A 136 LYS cc_start: 0.9227 (tptt) cc_final: 0.8904 (tptp) REVERT: A 140 TYR cc_start: 0.9230 (m-80) cc_final: 0.9023 (m-80) REVERT: A 144 MET cc_start: 0.9376 (mtm) cc_final: 0.9164 (mtp) REVERT: A 180 ASN cc_start: 0.8743 (m110) cc_final: 0.8467 (m110) REVERT: A 217 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9028 (mm-30) REVERT: A 250 TYR cc_start: 0.9354 (m-80) cc_final: 0.8698 (m-80) REVERT: A 263 ASP cc_start: 0.8796 (m-30) cc_final: 0.8436 (m-30) REVERT: A 274 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8295 (ttm170) REVERT: A 286 ASP cc_start: 0.8932 (m-30) cc_final: 0.8170 (m-30) REVERT: A 290 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 317 MET cc_start: 0.9119 (mtp) cc_final: 0.8861 (mtt) REVERT: A 362 ASP cc_start: 0.8603 (m-30) cc_final: 0.7935 (m-30) REVERT: A 379 SER cc_start: 0.9425 (t) cc_final: 0.9060 (t) REVERT: A 420 MET cc_start: 0.9514 (mmm) cc_final: 0.9298 (mmm) REVERT: A 458 MET cc_start: 0.9108 (mmm) cc_final: 0.8871 (mmt) REVERT: A 570 MET cc_start: 0.8897 (mtp) cc_final: 0.8604 (mtm) REVERT: A 686 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.7758 (mmm-85) REVERT: B 15 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 65 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8289 (mm-30) REVERT: B 66 GLU cc_start: 0.8535 (tp30) cc_final: 0.8245 (tp30) REVERT: B 104 TYR cc_start: 0.9280 (m-80) cc_final: 0.9078 (m-80) REVERT: B 144 MET cc_start: 0.9362 (mtm) cc_final: 0.8834 (mtp) REVERT: B 148 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8548 (mt-10) REVERT: B 238 ASP cc_start: 0.8182 (p0) cc_final: 0.7945 (t0) REVERT: B 266 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8263 (mtpp) REVERT: B 274 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8074 (ttm170) REVERT: B 296 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8416 (mmmt) REVERT: B 348 MET cc_start: 0.9320 (ttp) cc_final: 0.9010 (tmm) REVERT: B 402 GLU cc_start: 0.8915 (mp0) cc_final: 0.8578 (mp0) REVERT: B 447 ASN cc_start: 0.8341 (m110) cc_final: 0.8121 (m-40) REVERT: B 471 TYR cc_start: 0.9422 (t80) cc_final: 0.9132 (t80) REVERT: B 475 ASN cc_start: 0.9456 (m110) cc_final: 0.8939 (m-40) REVERT: B 493 MET cc_start: 0.9673 (tmm) cc_final: 0.9457 (tmm) REVERT: B 515 ASP cc_start: 0.9136 (m-30) cc_final: 0.8635 (m-30) REVERT: B 586 TYR cc_start: 0.9133 (m-80) cc_final: 0.8857 (m-80) REVERT: B 598 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (mtp) REVERT: B 602 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8054 (tt0) REVERT: B 610 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8853 (mtmm) REVERT: B 615 MET cc_start: 0.9600 (mmp) cc_final: 0.9277 (mmp) REVERT: B 662 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (mtm) REVERT: B 684 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: B 686 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8237 (mmm-85) REVERT: C 96 MET cc_start: 0.0036 (mmt) cc_final: -0.0246 (mmt) REVERT: C 137 MET cc_start: -0.0101 (mtp) cc_final: -0.0335 (mtp) REVERT: C 155 LYS cc_start: 0.4332 (mmtp) cc_final: 0.3981 (ptmt) REVERT: D 91 ASN cc_start: 0.1821 (m-40) cc_final: 0.1331 (t0) REVERT: D 269 MET cc_start: 0.3801 (tpt) cc_final: 0.3315 (mpp) REVERT: E 46 MET cc_start: 0.8632 (tpt) cc_final: 0.8164 (tpt) outliers start: 52 outliers final: 32 residues processed: 421 average time/residue: 0.1305 time to fit residues: 83.2211 Evaluate side-chains 408 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 370 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 153 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106484 restraints weight = 26392.908| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.18 r_work: 0.2937 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (21 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17041 Z= 0.162 Angle : 0.558 15.721 23026 Z= 0.290 Chirality : 0.042 0.236 2464 Planarity : 0.003 0.041 2931 Dihedral : 8.232 137.679 2375 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.91 % Allowed : 18.56 % Favored : 78.54 % 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: 1.52 (0.19), residues: 2012 helix: 1.68 (0.15), residues: 1176 sheet: -0.39 (0.42), residues: 157 loop : 0.33 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 184 TYR 0.034 0.001 TYR D 105 PHE 0.025 0.001 PHE C 227 TRP 0.013 0.001 TRP D 30 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (17038) covalent geometry : angle 0.55691 / 0.29 (23020) SS BOND : bond 0.00242 / 0.13 ( 3) SS BOND : angle 2.55059 / 1.36 ( 6) hydrogen bonds : bond 0.03603 / 2.29 ( 912) hydrogen bonds : angle 4.60507 / 3.17 ( 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 440 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 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: A 23 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (mmmm) REVERT: A 49 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8813 (t-90) REVERT: A 65 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7854 (mp0) REVERT: A 136 LYS cc_start: 0.9261 (tptt) cc_final: 0.8976 (tptp) REVERT: A 180 ASN cc_start: 0.8720 (m110) cc_final: 0.8479 (m-40) REVERT: A 217 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9016 (mm-30) REVERT: A 250 TYR cc_start: 0.9337 (m-80) cc_final: 0.8705 (m-80) REVERT: A 263 ASP cc_start: 0.8786 (m-30) cc_final: 0.8402 (m-30) REVERT: A 274 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8301 (ttm170) REVERT: A 286 ASP cc_start: 0.8901 (m-30) cc_final: 0.8126 (m-30) REVERT: A 290 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 317 MET cc_start: 0.9117 (mtp) cc_final: 0.8824 (mtt) REVERT: A 362 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 379 SER cc_start: 0.9413 (t) cc_final: 0.9061 (t) REVERT: A 420 MET cc_start: 0.9477 (mmm) cc_final: 0.9276 (mmm) REVERT: A 458 MET cc_start: 0.9116 (mmm) cc_final: 0.8880 (mmt) REVERT: A 570 MET cc_start: 0.8869 (mtp) cc_final: 0.8664 (mtp) REVERT: A 686 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7801 (mmm-85) REVERT: B 15 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 65 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8185 (mm-30) REVERT: B 66 GLU cc_start: 0.8463 (tp30) cc_final: 0.8156 (tp30) REVERT: B 104 TYR cc_start: 0.9276 (m-80) cc_final: 0.9055 (m-80) REVERT: B 144 MET cc_start: 0.9340 (mtm) cc_final: 0.8811 (mtp) REVERT: B 147 GLN cc_start: 0.9366 (mt0) cc_final: 0.9080 (mm-40) REVERT: B 266 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8294 (mtpp) REVERT: B 274 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7978 (ttm170) REVERT: B 296 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8551 (mmmt) REVERT: B 357 TYR cc_start: 0.9303 (m-10) cc_final: 0.8626 (m-80) REVERT: B 402 GLU cc_start: 0.8907 (mp0) cc_final: 0.8570 (mp0) REVERT: B 475 ASN cc_start: 0.9434 (m110) cc_final: 0.9062 (m-40) REVERT: B 493 MET cc_start: 0.9653 (tmm) cc_final: 0.9443 (tmm) REVERT: B 515 ASP cc_start: 0.9106 (m-30) cc_final: 0.8608 (m-30) REVERT: B 586 TYR cc_start: 0.9125 (m-80) cc_final: 0.8863 (m-80) REVERT: B 598 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: B 602 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8017 (tt0) REVERT: B 610 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8887 (mtmm) REVERT: B 615 MET cc_start: 0.9603 (mmp) cc_final: 0.9275 (mmp) REVERT: B 662 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: B 684 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: B 686 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8250 (mmm-85) REVERT: C 137 MET cc_start: -0.0008 (mtp) cc_final: -0.0246 (mtp) REVERT: D 91 ASN cc_start: 0.1713 (m-40) cc_final: 0.1065 (t0) REVERT: D 93 MET cc_start: 0.2106 (mmm) cc_final: 0.1716 (mmm) REVERT: D 96 MET cc_start: -0.1171 (tmm) cc_final: -0.2659 (ttt) REVERT: D 269 MET cc_start: 0.4051 (tpt) cc_final: 0.3571 (mpp) REVERT: E 46 MET cc_start: 0.8625 (tpt) cc_final: 0.8131 (tpt) outliers start: 52 outliers final: 31 residues processed: 418 average time/residue: 0.1314 time to fit residues: 83.1160 Evaluate side-chains 406 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 368 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 265 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.187002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107980 restraints weight = 26438.865| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.20 r_work: 0.2967 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17041 Z= 0.143 Angle : 0.565 14.330 23026 Z= 0.293 Chirality : 0.042 0.261 2464 Planarity : 0.003 0.043 2931 Dihedral : 8.110 137.652 2374 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.35 % Allowed : 18.56 % Favored : 78.09 % 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: 1.49 (0.19), residues: 2012 helix: 1.67 (0.15), residues: 1172 sheet: -0.39 (0.43), residues: 157 loop : 0.28 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.023 0.001 TYR D 105 PHE 0.034 0.001 PHE C 227 TRP 0.013 0.001 TRP C 44 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17038) covalent geometry : angle 0.56318 / 0.29 (23020) SS BOND : bond 0.00152 / 0.07 ( 3) SS BOND : angle 2.82025 / 1.51 ( 6) hydrogen bonds : bond 0.03533 / 2.23 ( 912) hydrogen bonds : angle 4.58267 / 3.15 ( 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 455 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 395 time to evaluate : 0.640 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: A 23 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8831 (mmmm) REVERT: A 29 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8933 (t70) REVERT: A 30 LYS cc_start: 0.8961 (tptp) cc_final: 0.8589 (tptt) REVERT: A 49 HIS cc_start: 0.9148 (OUTLIER) cc_final: 0.8787 (t-90) REVERT: A 65 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7810 (mp0) REVERT: A 136 LYS cc_start: 0.9236 (tptt) cc_final: 0.9012 (tptp) REVERT: A 144 MET cc_start: 0.9391 (mtm) cc_final: 0.9135 (mtp) REVERT: A 217 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9018 (mm-30) REVERT: A 250 TYR cc_start: 0.9346 (m-80) cc_final: 0.8707 (m-80) REVERT: A 263 ASP cc_start: 0.8781 (m-30) cc_final: 0.8386 (m-30) REVERT: A 274 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8267 (ttm-80) REVERT: A 286 ASP cc_start: 0.8899 (m-30) cc_final: 0.8061 (m-30) REVERT: A 290 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 316 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 317 MET cc_start: 0.9104 (mtp) cc_final: 0.8788 (mtt) REVERT: A 362 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: A 379 SER cc_start: 0.9405 (t) cc_final: 0.9048 (t) REVERT: A 420 MET cc_start: 0.9464 (mmm) cc_final: 0.9238 (mmm) REVERT: A 458 MET cc_start: 0.9103 (mmm) cc_final: 0.8836 (mmt) REVERT: A 645 GLN cc_start: 0.9146 (tp40) cc_final: 0.8925 (tp40) REVERT: A 662 MET cc_start: 0.9051 (ptp) cc_final: 0.8657 (ptp) REVERT: A 686 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.7763 (mmm-85) REVERT: B 15 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 44 ASN cc_start: 0.9210 (m110) cc_final: 0.8757 (m-40) REVERT: B 66 GLU cc_start: 0.8445 (tp30) cc_final: 0.8160 (tp30) REVERT: B 104 TYR cc_start: 0.9273 (m-80) cc_final: 0.9036 (m-80) REVERT: B 144 MET cc_start: 0.9323 (mtm) cc_final: 0.8764 (mtp) REVERT: B 147 GLN cc_start: 0.9346 (mt0) cc_final: 0.9085 (mm-40) REVERT: B 228 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8957 (mtmm) REVERT: B 235 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8867 (ttm110) REVERT: B 266 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8348 (mtpp) REVERT: B 274 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7999 (ttm170) REVERT: B 296 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8553 (mmmt) REVERT: B 357 TYR cc_start: 0.9260 (m-10) cc_final: 0.8600 (m-80) REVERT: B 475 ASN cc_start: 0.9424 (m110) cc_final: 0.9050 (m-40) REVERT: B 515 ASP cc_start: 0.9104 (m-30) cc_final: 0.8858 (m-30) REVERT: B 586 TYR cc_start: 0.9086 (m-80) cc_final: 0.8885 (m-80) REVERT: B 598 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: B 602 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8096 (tt0) REVERT: B 610 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8912 (mtmm) REVERT: B 615 MET cc_start: 0.9575 (mmp) cc_final: 0.9250 (mmp) REVERT: B 662 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: B 684 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: B 686 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: C 109 PHE cc_start: 0.5207 (m-10) cc_final: 0.4865 (m-10) REVERT: C 166 PHE cc_start: 0.2132 (m-80) cc_final: 0.1547 (m-80) REVERT: D 91 ASN cc_start: 0.1466 (m-40) cc_final: 0.0868 (t0) REVERT: D 96 MET cc_start: -0.1325 (tmm) cc_final: -0.2569 (ttt) REVERT: D 269 MET cc_start: 0.4037 (tpt) cc_final: 0.3596 (mpp) REVERT: E 46 MET cc_start: 0.8679 (tpt) cc_final: 0.8152 (tpt) outliers start: 60 outliers final: 34 residues processed: 429 average time/residue: 0.1342 time to fit residues: 86.6115 Evaluate side-chains 410 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 368 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 152 optimal weight: 30.0000 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 188 optimal weight: 30.0000 chunk 28 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.191378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116072 restraints weight = 26542.575| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.38 r_work: 0.3008 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17041 Z= 0.126 Angle : 0.566 13.190 23026 Z= 0.296 Chirality : 0.042 0.270 2464 Planarity : 0.003 0.041 2931 Dihedral : 7.937 137.718 2374 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.52 % Allowed : 19.68 % Favored : 77.81 % 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: 1.51 (0.19), residues: 2012 helix: 1.62 (0.15), residues: 1172 sheet: 0.37 (0.49), residues: 123 loop : 0.22 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 184 TYR 0.051 0.001 TYR D 179 PHE 0.031 0.001 PHE C 227 TRP 0.007 0.001 TRP C 44 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (17038) covalent geometry : angle 0.56455 / 0.30 (23020) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 2.36207 / 1.25 ( 6) hydrogen bonds : bond 0.03443 / 2.18 ( 912) hydrogen bonds : angle 4.57156 / 3.15 ( 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 446 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 401 time to evaluate : 0.649 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: A 23 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8801 (mmmm) REVERT: A 29 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8908 (t70) REVERT: A 30 LYS cc_start: 0.8942 (tptp) cc_final: 0.8566 (tptt) REVERT: A 65 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7716 (mp0) REVERT: A 144 MET cc_start: 0.9350 (mtm) cc_final: 0.9096 (mtp) REVERT: A 217 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9045 (mm-30) REVERT: A 250 TYR cc_start: 0.9317 (m-80) cc_final: 0.8730 (m-80) REVERT: A 257 ASP cc_start: 0.9110 (m-30) cc_final: 0.8887 (m-30) REVERT: A 286 ASP cc_start: 0.8742 (m-30) cc_final: 0.8016 (m-30) REVERT: A 290 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 317 MET cc_start: 0.8944 (mtp) cc_final: 0.8650 (mtp) REVERT: A 362 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: A 379 SER cc_start: 0.9409 (t) cc_final: 0.9052 (t) REVERT: A 420 MET cc_start: 0.9470 (mmm) cc_final: 0.9241 (mmm) REVERT: A 458 MET cc_start: 0.9071 (mmm) cc_final: 0.8768 (mmt) REVERT: A 645 GLN cc_start: 0.9127 (tp40) cc_final: 0.8863 (tp40) REVERT: A 662 MET cc_start: 0.8983 (ptp) cc_final: 0.8555 (ptp) REVERT: A 686 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8145 (ttm-80) REVERT: B 15 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8592 (mm-30) REVERT: B 44 ASN cc_start: 0.9170 (m110) cc_final: 0.8732 (m-40) REVERT: B 66 GLU cc_start: 0.8326 (tp30) cc_final: 0.7904 (tp30) REVERT: B 104 TYR cc_start: 0.9253 (m-80) cc_final: 0.9010 (m-80) REVERT: B 117 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8837 (mtp85) REVERT: B 144 MET cc_start: 0.9269 (mtm) cc_final: 0.8677 (mtp) REVERT: B 228 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8956 (mtmm) REVERT: B 235 ARG cc_start: 0.9071 (ttm-80) cc_final: 0.8777 (mtm-85) REVERT: B 240 MET cc_start: 0.7037 (ppp) cc_final: 0.6762 (ppp) REVERT: B 266 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8176 (mtpp) REVERT: B 274 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8043 (ttm170) REVERT: B 296 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8494 (mmmt) REVERT: B 315 ASP cc_start: 0.8372 (p0) cc_final: 0.8067 (p0) REVERT: B 357 TYR cc_start: 0.9202 (m-10) cc_final: 0.8580 (m-80) REVERT: B 370 ASN cc_start: 0.9464 (m-40) cc_final: 0.9066 (m110) REVERT: B 471 TYR cc_start: 0.9268 (t80) cc_final: 0.8991 (t80) REVERT: B 475 ASN cc_start: 0.9390 (m110) cc_final: 0.8805 (m-40) REVERT: B 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8893 (m-30) REVERT: B 556 GLU cc_start: 0.9037 (mp0) cc_final: 0.8803 (mp0) REVERT: B 570 MET cc_start: 0.8672 (ttp) cc_final: 0.8446 (ttm) REVERT: B 598 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8520 (mtp) REVERT: B 602 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8300 (tt0) REVERT: B 604 ARG cc_start: 0.9249 (mmm160) cc_final: 0.8715 (mmm160) REVERT: B 632 MET cc_start: 0.8964 (mtp) cc_final: 0.8639 (ttm) REVERT: B 659 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8523 (mttp) REVERT: B 684 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: B 686 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8237 (mmm-85) REVERT: C 96 MET cc_start: 0.0499 (mmt) cc_final: 0.0294 (mmt) REVERT: C 109 PHE cc_start: 0.4859 (m-10) cc_final: 0.4639 (m-10) REVERT: C 110 MET cc_start: 0.5865 (mpp) cc_final: 0.5624 (pmm) REVERT: C 166 PHE cc_start: 0.2065 (m-80) cc_final: 0.1586 (m-80) REVERT: C 269 MET cc_start: 0.5772 (tpp) cc_final: 0.5321 (ptt) REVERT: D 91 ASN cc_start: 0.1281 (m-40) cc_final: 0.0860 (t0) REVERT: D 96 MET cc_start: -0.1604 (tmm) cc_final: -0.2178 (ttt) REVERT: D 137 MET cc_start: 0.3486 (tpt) cc_final: 0.2981 (mtm) REVERT: D 269 MET cc_start: 0.4194 (tpt) cc_final: 0.3784 (mpp) REVERT: D 287 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5773 (pt) REVERT: E 46 MET cc_start: 0.8617 (tpt) cc_final: 0.8084 (tpt) outliers start: 45 outliers final: 29 residues processed: 424 average time/residue: 0.1340 time to fit residues: 85.9344 Evaluate side-chains 410 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 127 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.189456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117186 restraints weight = 26619.358| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.19 r_work: 0.2989 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17041 Z= 0.156 Angle : 0.607 12.995 23026 Z= 0.314 Chirality : 0.043 0.255 2464 Planarity : 0.003 0.041 2931 Dihedral : 7.860 138.691 2373 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.46 % Allowed : 20.91 % Favored : 76.63 % 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: 1.30 (0.18), residues: 2012 helix: 1.52 (0.15), residues: 1195 sheet: 0.11 (0.53), residues: 103 loop : -0.04 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.051 0.001 TYR D 179 PHE 0.029 0.002 PHE C 227 TRP 0.009 0.001 TRP D 30 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17038) covalent geometry : angle 0.60545 / 0.31 (23020) SS BOND : bond 0.00350 / 0.18 ( 3) SS BOND : angle 2.58170 / 1.38 ( 6) hydrogen bonds : bond 0.03444 / 2.17 ( 912) hydrogen bonds : angle 4.56024 / 3.14 ( 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 421 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 377 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9259 (t0) cc_final: 0.8931 (t70) REVERT: A 30 LYS cc_start: 0.8823 (tptp) cc_final: 0.8519 (tptt) REVERT: A 65 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7847 (mp0) REVERT: A 144 MET cc_start: 0.9355 (mtm) cc_final: 0.9092 (mtp) REVERT: A 217 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9091 (mm-30) REVERT: A 250 TYR cc_start: 0.9347 (m-80) cc_final: 0.8749 (m-80) REVERT: A 286 ASP cc_start: 0.8726 (m-30) cc_final: 0.8014 (m-30) REVERT: A 290 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 317 MET cc_start: 0.8998 (mtp) cc_final: 0.8717 (mtp) REVERT: A 326 PHE cc_start: 0.9446 (m-10) cc_final: 0.9106 (m-10) REVERT: A 334 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8165 (ptpp) REVERT: A 362 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: A 458 MET cc_start: 0.9094 (mmm) cc_final: 0.8805 (mmt) REVERT: B 11 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8787 (pt0) REVERT: B 15 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 44 ASN cc_start: 0.9099 (m110) cc_final: 0.8633 (m-40) REVERT: B 65 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8090 (mp0) REVERT: B 66 GLU cc_start: 0.8294 (tp30) cc_final: 0.7839 (tp30) REVERT: B 117 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8839 (mtp85) REVERT: B 144 MET cc_start: 0.9290 (mtm) cc_final: 0.8733 (mtp) REVERT: B 228 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8976 (mtmm) REVERT: B 266 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8203 (mtpp) REVERT: B 274 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8077 (ttm170) REVERT: B 296 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8507 (mmmt) REVERT: B 357 TYR cc_start: 0.9248 (m-10) cc_final: 0.8630 (m-80) REVERT: B 370 ASN cc_start: 0.9517 (m-40) cc_final: 0.9139 (m-40) REVERT: B 415 ASN cc_start: 0.9140 (t0) cc_final: 0.8788 (t0) REVERT: B 471 TYR cc_start: 0.9344 (t80) cc_final: 0.9069 (t80) REVERT: B 475 ASN cc_start: 0.9423 (m110) cc_final: 0.8865 (m-40) REVERT: B 515 ASP cc_start: 0.9101 (m-30) cc_final: 0.8897 (m-30) REVERT: B 570 MET cc_start: 0.8842 (ttp) cc_final: 0.8614 (ttm) REVERT: B 598 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: B 602 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8578 (tt0) REVERT: B 610 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8819 (ptpp) REVERT: B 615 MET cc_start: 0.9605 (OUTLIER) cc_final: 0.9148 (mmp) REVERT: B 632 MET cc_start: 0.8897 (mtp) cc_final: 0.8529 (ttm) REVERT: B 662 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7602 (mpp) REVERT: B 684 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7312 (m-10) REVERT: B 686 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: C 50 ASN cc_start: 0.5674 (p0) cc_final: 0.5409 (m-40) REVERT: C 96 MET cc_start: 0.0329 (mmt) cc_final: 0.0113 (mmt) REVERT: C 109 PHE cc_start: 0.4934 (m-10) cc_final: 0.4674 (m-10) REVERT: C 110 MET cc_start: 0.5882 (mpp) cc_final: 0.5674 (pmm) REVERT: C 166 PHE cc_start: 0.2229 (m-80) cc_final: 0.1790 (m-80) REVERT: C 269 MET cc_start: 0.5634 (tpp) cc_final: 0.5227 (ptt) REVERT: D 91 ASN cc_start: 0.1558 (m-40) cc_final: 0.1040 (t0) REVERT: D 269 MET cc_start: 0.4237 (tpt) cc_final: 0.3859 (mpp) REVERT: E 34 MET cc_start: 0.8481 (ppp) cc_final: 0.8243 (ppp) REVERT: E 46 MET cc_start: 0.8669 (tpt) cc_final: 0.8120 (tpt) outliers start: 44 outliers final: 32 residues processed: 405 average time/residue: 0.1316 time to fit residues: 80.7466 Evaluate side-chains 403 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 158 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111935 restraints weight = 26296.615| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.34 r_work: 0.2997 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17041 Z= 0.132 Angle : 0.612 13.040 23026 Z= 0.315 Chirality : 0.043 0.318 2464 Planarity : 0.003 0.044 2931 Dihedral : 7.730 138.992 2373 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.79 % Allowed : 21.80 % Favored : 76.41 % 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: 1.19 (0.18), residues: 2012 helix: 1.43 (0.15), residues: 1197 sheet: 0.14 (0.53), residues: 103 loop : -0.10 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.024 0.001 TYR C 22 PHE 0.030 0.001 PHE C 227 TRP 0.007 0.001 TRP D 30 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (17038) covalent geometry : angle 0.61075 / 0.31 (23020) SS BOND : bond 0.00278 / 0.14 ( 3) SS BOND : angle 2.13538 / 1.14 ( 6) hydrogen bonds : bond 0.03398 / 2.12 ( 912) hydrogen bonds : angle 4.56570 / 3.16 ( 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 410 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9241 (t0) cc_final: 0.8897 (t70) REVERT: A 30 LYS cc_start: 0.8812 (tptp) cc_final: 0.8552 (tptt) REVERT: A 65 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7675 (mp0) REVERT: A 144 MET cc_start: 0.9312 (mtm) cc_final: 0.9027 (mtp) REVERT: A 250 TYR cc_start: 0.9355 (m-80) cc_final: 0.8767 (m-80) REVERT: A 257 ASP cc_start: 0.9110 (m-30) cc_final: 0.8872 (m-30) REVERT: A 276 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8843 (mmtt) REVERT: A 286 ASP cc_start: 0.8791 (m-30) cc_final: 0.8095 (m-30) REVERT: A 290 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 317 MET cc_start: 0.9051 (mtp) cc_final: 0.8634 (mtt) REVERT: A 326 PHE cc_start: 0.9423 (m-10) cc_final: 0.9175 (m-10) REVERT: A 362 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: A 402 GLU cc_start: 0.8728 (mp0) cc_final: 0.8485 (mp0) REVERT: A 458 MET cc_start: 0.9061 (mmm) cc_final: 0.8767 (mmt) REVERT: A 493 MET cc_start: 0.9222 (tmm) cc_final: 0.9020 (tmm) REVERT: B 15 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 44 ASN cc_start: 0.9134 (m110) cc_final: 0.8720 (m-40) REVERT: B 65 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8163 (mp0) REVERT: B 66 GLU cc_start: 0.8277 (tp30) cc_final: 0.7754 (tp30) REVERT: B 228 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8964 (mtmm) REVERT: B 235 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8896 (ttm110) REVERT: B 266 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8547 (mtpp) REVERT: B 274 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8441 (ttm-80) REVERT: B 296 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8461 (mmmt) REVERT: B 357 TYR cc_start: 0.9162 (m-10) cc_final: 0.8565 (m-80) REVERT: B 370 ASN cc_start: 0.9531 (m-40) cc_final: 0.9071 (m110) REVERT: B 475 ASN cc_start: 0.9263 (m110) cc_final: 0.8907 (m-40) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8859 (m-30) REVERT: B 556 GLU cc_start: 0.9055 (mp0) cc_final: 0.8814 (mp0) REVERT: B 602 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8755 (tt0) REVERT: B 604 ARG cc_start: 0.9253 (mmm160) cc_final: 0.8889 (mmm160) REVERT: B 610 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8825 (ptpp) REVERT: B 662 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: B 684 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: B 686 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8282 (mmm-85) REVERT: C 50 ASN cc_start: 0.5556 (p0) cc_final: 0.5267 (m-40) REVERT: C 96 MET cc_start: 0.0232 (mmt) cc_final: -0.0001 (mmt) REVERT: C 166 PHE cc_start: 0.2123 (m-80) cc_final: 0.1854 (m-80) REVERT: C 257 LYS cc_start: 0.2692 (mtmt) cc_final: 0.2178 (tppt) REVERT: C 269 MET cc_start: 0.5597 (tpp) cc_final: 0.5190 (ptt) REVERT: D 91 ASN cc_start: 0.1491 (m-40) cc_final: 0.0944 (t0) REVERT: D 137 MET cc_start: 0.3588 (tpt) cc_final: 0.3060 (mtm) REVERT: D 269 MET cc_start: 0.4064 (tpt) cc_final: 0.3683 (mpp) REVERT: E 34 MET cc_start: 0.8476 (ppp) cc_final: 0.8252 (ppp) REVERT: E 46 MET cc_start: 0.8652 (tpt) cc_final: 0.8119 (tpt) outliers start: 32 outliers final: 25 residues processed: 398 average time/residue: 0.1308 time to fit residues: 78.2921 Evaluate side-chains 390 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 361 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 304 HIS B 232 ASN B 418 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.191235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113174 restraints weight = 26667.143| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.25 r_work: 0.2995 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17041 Z= 0.144 Angle : 0.631 13.757 23026 Z= 0.322 Chirality : 0.044 0.322 2464 Planarity : 0.004 0.044 2931 Dihedral : 7.658 138.866 2373 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.01 % Allowed : 22.19 % Favored : 75.80 % 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: 1.16 (0.18), residues: 2012 helix: 1.42 (0.15), residues: 1197 sheet: 0.35 (0.65), residues: 73 loop : -0.15 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.075 0.002 TYR D 179 PHE 0.049 0.002 PHE C 109 TRP 0.005 0.001 TRP A 558 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (17038) covalent geometry : angle 0.63012 / 0.32 (23020) SS BOND : bond 0.00320 / 0.17 ( 3) SS BOND : angle 2.34805 / 1.26 ( 6) hydrogen bonds : bond 0.03413 / 2.14 ( 912) hydrogen bonds : angle 4.58078 / 3.17 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5302.81 seconds wall clock time: 91 minutes 35.73 seconds (5495.73 seconds total)