Starting phenix.real_space_refine on Fri Jul 3 22:04:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxs_45010/07_2026/9bxs_45010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxs_45010/07_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_45010/07_2026/9bxs_45010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxs_45010/07_2026/9bxs_45010.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxs_45010/07_2026/9bxs_45010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxs_45010/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.99, per 1000 atoms: 0.24 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: 1.39 Conformation dependent library (CDL) restraints added in 897.3 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: 0.58 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: 2.98 Time building geometry restraints manager: 1.88 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 3.060 ... (remaining 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: 1.600 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 : 0.650 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: 0.1317 time to fit residues: 126.8253 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 : 0.593 ------------------------------------------------------------------------------- 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 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN D 69 GLN D 80 HIS D 132 GLN D 201 HIS ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.184112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109868 restraints weight = 25274.678| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.08 r_work: 0.2925 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 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 = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17041 Z= 0.267 Angle : 0.659 17.117 23026 Z= 0.345 Chirality : 0.045 0.169 2464 Planarity : 0.004 0.042 2931 Dihedral : 9.247 136.183 2389 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.96 % Allowed : 17.72 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2012 helix: 1.48 (0.15), residues: 1166 sheet: -0.07 (0.41), residues: 153 loop : 0.46 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.020 0.002 TYR A 140 PHE 0.018 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 0.00591 / 0.27 (17038) covalent geometry : angle 0.65776 / 0.34 (23020) SS BOND : bond 0.00654 / 0.25 ( 3) SS BOND : angle 2.73818 / 1.49 ( 6) hydrogen bonds : bond 0.04659 / 3.00 ( 912) hydrogen bonds : angle 4.93309 / 3.39 ( 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 479 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 426 time to evaluate : 0.617 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: 0.9068 (OUTLIER) cc_final: 0.8798 (mmmm) REVERT: A 29 ASP cc_start: 0.9353 (t0) cc_final: 0.8957 (t70) REVERT: A 49 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.8737 (t-90) REVERT: A 65 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8019 (mp0) REVERT: A 191 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8966 (mm-40) REVERT: A 209 LYS cc_start: 0.9283 (ttpp) cc_final: 0.9073 (ttmm) REVERT: A 217 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8916 (mm-30) REVERT: A 250 TYR cc_start: 0.9313 (m-80) cc_final: 0.8785 (m-80) REVERT: A 263 ASP cc_start: 0.8914 (m-30) cc_final: 0.8403 (m-30) REVERT: A 286 ASP cc_start: 0.8894 (m-30) cc_final: 0.8253 (m-30) REVERT: A 352 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8710 (mt-10) REVERT: A 362 ASP cc_start: 0.8479 (m-30) cc_final: 0.7968 (m-30) REVERT: A 379 SER cc_start: 0.9436 (t) cc_final: 0.9039 (t) REVERT: A 586 TYR cc_start: 0.9317 (m-80) cc_final: 0.9077 (m-80) REVERT: A 598 MET cc_start: 0.9313 (mtm) cc_final: 0.8979 (mtt) REVERT: A 686 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7941 (ttm-80) REVERT: B 11 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8778 (pt0) REVERT: B 15 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 65 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8391 (mm-30) REVERT: B 104 TYR cc_start: 0.9234 (m-80) cc_final: 0.8823 (m-80) REVERT: B 148 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8585 (mt-10) REVERT: B 150 GLN cc_start: 0.9237 (tp40) cc_final: 0.8694 (tp-100) REVERT: B 177 ASP cc_start: 0.8855 (t0) cc_final: 0.8594 (t70) REVERT: B 243 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5556 (ttt180) REVERT: B 266 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8360 (mtpp) REVERT: B 274 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8385 (ttm-80) REVERT: B 296 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8395 (mmmt) REVERT: B 321 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8438 (tm-30) REVERT: B 333 LYS cc_start: 0.9396 (tttt) cc_final: 0.9049 (mtpp) REVERT: B 493 MET cc_start: 0.9640 (tmm) cc_final: 0.9357 (tmm) REVERT: B 515 ASP cc_start: 0.9111 (m-30) cc_final: 0.8695 (m-30) REVERT: B 586 TYR cc_start: 0.9239 (m-80) cc_final: 0.8779 (m-80) REVERT: B 588 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8542 (mm-40) REVERT: B 602 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8100 (tt0) REVERT: B 615 MET cc_start: 0.9543 (mmp) cc_final: 0.9252 (mmp) REVERT: B 662 MET cc_start: 0.8521 (ptp) cc_final: 0.8286 (ptp) REVERT: B 686 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8219 (mtp85) REVERT: C 95 MET cc_start: 0.0901 (ppp) cc_final: 0.0638 (ppp) REVERT: C 130 TYR cc_start: 0.6752 (m-80) cc_final: 0.6456 (m-10) REVERT: C 137 MET cc_start: -0.0170 (mtp) cc_final: -0.0379 (mtp) REVERT: C 155 LYS cc_start: 0.4132 (mmtp) cc_final: 0.3523 (ptmt) REVERT: D 91 ASN cc_start: 0.2333 (m-40) cc_final: 0.1749 (t0) REVERT: D 185 MET cc_start: 0.7333 (mmm) cc_final: 0.7047 (mmm) REVERT: D 189 GLU cc_start: 0.6065 (tt0) cc_final: 0.5549 (pt0) REVERT: E 46 MET cc_start: 0.8682 (tpt) cc_final: 0.8357 (tpt) outliers start: 53 outliers final: 20 residues processed: 460 average time/residue: 0.1260 time to fit residues: 87.1713 Evaluate side-chains 400 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 375 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 499 SER Chi-restraints excluded: chain B residue 584 ILE 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: 0.8980 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 130 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4155 r_free = 0.4155 target = 0.185276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105644 restraints weight = 26199.158| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.14 r_work: 0.2936 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- 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: 1 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17041 Z= 0.143 Angle : 0.564 14.573 23026 Z= 0.294 Chirality : 0.042 0.173 2464 Planarity : 0.003 0.043 2931 Dihedral : 8.638 133.698 2379 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.79 % Allowed : 17.55 % Favored : 79.65 % 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: 1.56 (0.19), residues: 2012 helix: 1.62 (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 0.004 0.001 ARG A 686 TYR 0.018 0.001 TYR A 140 PHE 0.019 0.001 PHE C 259 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 0.00314 / 0.14 (17038) covalent geometry : angle 0.56288 / 0.29 (23020) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 2.03780 / 1.10 ( 6) hydrogen bonds : bond 0.04047 / 2.59 ( 912) hydrogen bonds : angle 4.71054 / 3.23 ( 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 476 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 426 time to evaluate : 0.643 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: 0.9076 (OUTLIER) cc_final: 0.8841 (mmmm) REVERT: A 29 ASP cc_start: 0.9290 (t0) cc_final: 0.8890 (t70) REVERT: A 49 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8846 (t-90) REVERT: A 65 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7556 (mp0) REVERT: A 136 LYS cc_start: 0.9287 (tptt) cc_final: 0.8931 (tptp) REVERT: A 217 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8873 (mm-30) REVERT: A 250 TYR cc_start: 0.9343 (m-80) cc_final: 0.8836 (m-80) REVERT: A 263 ASP cc_start: 0.8772 (m-30) cc_final: 0.8315 (m-30) REVERT: A 286 ASP cc_start: 0.8867 (m-30) cc_final: 0.8180 (m-30) REVERT: A 290 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 352 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 362 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 379 SER cc_start: 0.9431 (t) cc_final: 0.9045 (t) REVERT: A 385 VAL cc_start: 0.9374 (t) cc_final: 0.9151 (p) REVERT: A 602 GLU cc_start: 0.8678 (tt0) cc_final: 0.7720 (tt0) REVERT: A 604 ARG cc_start: 0.8840 (mmp80) cc_final: 0.8556 (mmp80) REVERT: A 639 ASP cc_start: 0.9252 (m-30) cc_final: 0.8998 (m-30) REVERT: B 15 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 65 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8324 (mm-30) REVERT: B 104 TYR cc_start: 0.9158 (m-80) cc_final: 0.8770 (m-80) REVERT: B 106 LEU cc_start: 0.9300 (tp) cc_final: 0.9046 (tp) REVERT: B 150 GLN cc_start: 0.9145 (tp40) cc_final: 0.8929 (tp-100) REVERT: B 158 ASN cc_start: 0.9346 (m-40) cc_final: 0.9106 (m-40) REVERT: B 296 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8218 (mmmt) REVERT: B 333 LYS cc_start: 0.9312 (tttt) cc_final: 0.8998 (mtpp) REVERT: B 402 GLU cc_start: 0.8820 (mp0) cc_final: 0.8448 (mp0) REVERT: B 436 LEU cc_start: 0.9545 (mt) cc_final: 0.9262 (mt) REVERT: B 493 MET cc_start: 0.9654 (tmm) cc_final: 0.9308 (tmm) REVERT: B 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8627 (m-30) REVERT: B 586 TYR cc_start: 0.9218 (m-80) cc_final: 0.8871 (m-80) REVERT: B 598 MET cc_start: 0.8889 (mtp) cc_final: 0.8660 (mtp) REVERT: B 602 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8213 (tt0) REVERT: B 662 MET cc_start: 0.8504 (ptp) cc_final: 0.8248 (ptp) REVERT: B 684 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 686 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7922 (mtp85) REVERT: C 130 TYR cc_start: 0.6870 (m-80) cc_final: 0.6586 (m-10) REVERT: C 137 MET cc_start: -0.0013 (mtp) cc_final: -0.0245 (mtp) REVERT: C 155 LYS cc_start: 0.4187 (mmtp) cc_final: 0.3689 (ptmt) REVERT: D 91 ASN cc_start: 0.1841 (m-40) cc_final: 0.1145 (t0) REVERT: D 168 PHE cc_start: 0.2263 (OUTLIER) cc_final: 0.1779 (m-80) REVERT: D 269 MET cc_start: 0.3717 (tpt) cc_final: 0.3144 (mpp) REVERT: E 46 MET cc_start: 0.8746 (tpt) cc_final: 0.8299 (tpt) outliers start: 50 outliers final: 25 residues processed: 454 average time/residue: 0.1309 time to fit residues: 89.4644 Evaluate side-chains 411 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 168 PHE 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: 0.9980 chunk 85 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 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 24 GLN D 28 GLN D 201 HIS D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.185435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106591 restraints weight = 26135.095| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.29 r_work: 0.2898 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17041 Z= 0.211 Angle : 0.588 13.570 23026 Z= 0.308 Chirality : 0.043 0.169 2464 Planarity : 0.003 0.043 2931 Dihedral : 8.478 136.055 2375 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.30 % Allowed : 17.89 % Favored : 78.81 % 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: 1.53 (0.19), residues: 2012 helix: 1.62 (0.15), residues: 1171 sheet: -0.11 (0.41), residues: 153 loop : 0.38 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 207 TYR 0.024 0.002 TYR D 105 PHE 0.020 0.002 PHE D 92 TRP 0.008 0.001 TRP A 558 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (17038) covalent geometry : angle 0.58618 / 0.31 (23020) SS BOND : bond 0.00127 / 0.07 ( 3) SS BOND : angle 2.75103 / 1.49 ( 6) hydrogen bonds : bond 0.03970 / 2.51 ( 912) hydrogen bonds : angle 4.67556 / 3.20 ( 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 439 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 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: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8835 (mmmm) REVERT: A 30 LYS cc_start: 0.8921 (tptp) cc_final: 0.8675 (tptt) REVERT: A 49 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8890 (t-90) REVERT: A 65 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 136 LYS cc_start: 0.9271 (tptt) cc_final: 0.8982 (tptp) REVERT: A 217 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8906 (mm-30) REVERT: A 250 TYR cc_start: 0.9372 (m-80) cc_final: 0.8675 (m-80) REVERT: A 263 ASP cc_start: 0.8790 (m-30) cc_final: 0.8378 (m-30) REVERT: A 286 ASP cc_start: 0.8909 (m-30) cc_final: 0.8190 (m-30) REVERT: A 290 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 352 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8724 (mt-10) REVERT: A 362 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: A 379 SER cc_start: 0.9418 (t) cc_final: 0.8999 (t) REVERT: A 420 MET cc_start: 0.9505 (mmm) cc_final: 0.9302 (mmm) REVERT: A 458 MET cc_start: 0.9130 (mmm) cc_final: 0.8886 (mmt) REVERT: A 570 MET cc_start: 0.8986 (mtp) cc_final: 0.8681 (mtm) REVERT: A 598 MET cc_start: 0.9353 (mtm) cc_final: 0.8713 (mtm) REVERT: A 602 GLU cc_start: 0.8700 (tt0) cc_final: 0.7912 (tt0) REVERT: A 604 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8410 (mmp80) REVERT: B 15 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 21 ASP cc_start: 0.9120 (t0) cc_final: 0.8642 (t0) REVERT: B 65 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8342 (mm-30) REVERT: B 104 TYR cc_start: 0.9299 (m-80) cc_final: 0.9008 (m-80) REVERT: B 106 LEU cc_start: 0.9337 (tp) cc_final: 0.9104 (tp) REVERT: B 144 MET cc_start: 0.9396 (mtm) cc_final: 0.8905 (mtp) REVERT: B 147 GLN cc_start: 0.9389 (mt0) cc_final: 0.8997 (mt0) REVERT: B 266 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8293 (mtpp) REVERT: B 274 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8156 (ttm170) REVERT: B 296 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8336 (mmmt) REVERT: B 333 LYS cc_start: 0.9331 (tttt) cc_final: 0.9006 (mtpp) REVERT: B 402 GLU cc_start: 0.8886 (mp0) cc_final: 0.8525 (mp0) REVERT: B 471 TYR cc_start: 0.9395 (t80) cc_final: 0.9057 (t80) REVERT: B 475 ASN cc_start: 0.9507 (m110) cc_final: 0.9046 (m-40) REVERT: B 493 MET cc_start: 0.9691 (tmm) cc_final: 0.9385 (tmm) REVERT: B 515 ASP cc_start: 0.9147 (m-30) cc_final: 0.8650 (m-30) REVERT: B 586 TYR cc_start: 0.9240 (m-80) cc_final: 0.8857 (m-80) REVERT: B 602 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8134 (tt0) REVERT: B 615 MET cc_start: 0.9593 (mmp) cc_final: 0.9266 (mmp) REVERT: B 662 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (ptp) REVERT: B 684 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: B 686 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8205 (mmm-85) REVERT: C 130 TYR cc_start: 0.6964 (m-80) cc_final: 0.6689 (m-10) REVERT: C 137 MET cc_start: 0.0038 (mtp) cc_final: -0.0179 (mtp) REVERT: C 155 LYS cc_start: 0.4247 (mmtp) cc_final: 0.3726 (ptmt) REVERT: D 91 ASN cc_start: 0.1832 (m-40) cc_final: 0.1185 (t0) REVERT: D 93 MET cc_start: 0.2895 (mmt) cc_final: 0.2537 (mmm) REVERT: D 96 MET cc_start: -0.0323 (ppp) cc_final: -0.2631 (ttp) REVERT: D 269 MET cc_start: 0.3388 (tpt) cc_final: 0.2871 (mpp) REVERT: E 46 MET cc_start: 0.8678 (tpt) cc_final: 0.8222 (tpt) outliers start: 59 outliers final: 37 residues processed: 418 average time/residue: 0.1217 time to fit residues: 77.0281 Evaluate side-chains 414 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 371 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 11 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 200 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 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR 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 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: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 172 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 239 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 588 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.182718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106935 restraints weight = 26150.311| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.09 r_work: 0.2928 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17041 Z= 0.245 Angle : 0.594 15.908 23026 Z= 0.311 Chirality : 0.044 0.198 2464 Planarity : 0.003 0.041 2931 Dihedral : 8.543 138.212 2375 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.30 % Allowed : 17.78 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2012 helix: 1.56 (0.15), residues: 1190 sheet: -0.31 (0.41), residues: 153 loop : 0.27 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.026 0.002 TYR A 606 PHE 0.024 0.002 PHE C 92 TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (17038) covalent geometry : angle 0.59280 / 0.31 (23020) SS BOND : bond 0.00098 / 0.05 ( 3) SS BOND : angle 2.75562 / 1.50 ( 6) hydrogen bonds : bond 0.03860 / 2.46 ( 912) hydrogen bonds : angle 4.65264 / 3.20 ( 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 442 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 383 time to evaluate : 0.583 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: A 23 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8760 (mmmm) REVERT: A 49 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8748 (t-90) REVERT: A 65 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7988 (mp0) REVERT: A 191 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8789 (mm-40) REVERT: A 217 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8894 (mm-30) REVERT: A 250 TYR cc_start: 0.9360 (m-80) cc_final: 0.9043 (m-80) REVERT: A 263 ASP cc_start: 0.8793 (m-30) cc_final: 0.8394 (m-30) REVERT: A 274 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8219 (ttm-80) REVERT: A 286 ASP cc_start: 0.8897 (m-30) cc_final: 0.8174 (m-30) REVERT: A 290 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 362 ASP cc_start: 0.8601 (m-30) cc_final: 0.7955 (m-30) REVERT: A 379 SER cc_start: 0.9364 (t) cc_final: 0.9133 (t) REVERT: A 420 MET cc_start: 0.9418 (mmm) cc_final: 0.9199 (mmm) REVERT: A 447 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: A 570 MET cc_start: 0.8853 (mtp) cc_final: 0.8609 (mtm) REVERT: A 602 GLU cc_start: 0.8468 (tt0) cc_final: 0.7737 (tt0) REVERT: A 604 ARG cc_start: 0.8724 (mmp80) cc_final: 0.8255 (mmt-90) REVERT: A 686 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7808 (mmm-85) REVERT: B 15 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 23 LYS cc_start: 0.9154 (mptt) cc_final: 0.8744 (mmtt) REVERT: B 65 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8384 (mm-30) REVERT: B 104 TYR cc_start: 0.9286 (m-80) cc_final: 0.8998 (m-80) REVERT: B 106 LEU cc_start: 0.9357 (tp) cc_final: 0.9099 (tp) REVERT: B 144 MET cc_start: 0.9386 (mtm) cc_final: 0.8890 (mtp) REVERT: B 150 GLN cc_start: 0.9113 (tp40) cc_final: 0.8605 (tp-100) REVERT: B 266 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8394 (mtpp) REVERT: B 274 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8126 (ttm170) REVERT: B 296 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8470 (mmmt) REVERT: B 333 LYS cc_start: 0.9348 (tttt) cc_final: 0.9025 (mtpp) REVERT: B 402 GLU cc_start: 0.8865 (mp0) cc_final: 0.8488 (mp0) REVERT: B 475 ASN cc_start: 0.9464 (m110) cc_final: 0.8985 (m-40) REVERT: B 493 MET cc_start: 0.9655 (tmm) cc_final: 0.9407 (tmm) REVERT: B 515 ASP cc_start: 0.9114 (m-30) cc_final: 0.8908 (m-30) REVERT: B 586 TYR cc_start: 0.9189 (m-80) cc_final: 0.8829 (m-80) REVERT: B 602 GLU cc_start: 0.8756 (mt-10) cc_final: 0.7884 (tt0) REVERT: B 610 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8805 (mtmm) REVERT: B 615 MET cc_start: 0.9626 (mmp) cc_final: 0.9246 (mmp) REVERT: B 662 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: B 684 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: C 137 MET cc_start: 0.0006 (mtp) cc_final: -0.0229 (mtp) REVERT: C 155 LYS cc_start: 0.4071 (mmtp) cc_final: 0.3640 (ptmt) REVERT: D 91 ASN cc_start: 0.1950 (m-40) cc_final: 0.1457 (t0) REVERT: D 269 MET cc_start: 0.3846 (tpt) cc_final: 0.3399 (mpp) REVERT: E 46 MET cc_start: 0.8646 (tpt) cc_final: 0.8161 (tpt) outliers start: 59 outliers final: 39 residues processed: 420 average time/residue: 0.1211 time to fit residues: 76.8491 Evaluate side-chains 403 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 169 SER 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 349 LEU 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 447 ASN 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 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 200 SER Chi-restraints excluded: chain B residue 215 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 431 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 660 ASP 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 C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 184 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: 9.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 175 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 645 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.185517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106266 restraints weight = 26435.934| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.17 r_work: 0.2942 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 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 (9 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17041 Z= 0.141 Angle : 0.557 16.342 23026 Z= 0.291 Chirality : 0.042 0.235 2464 Planarity : 0.003 0.046 2931 Dihedral : 8.304 137.433 2375 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.91 % Allowed : 18.61 % Favored : 78.48 % 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: 1.39 (0.19), residues: 2012 helix: 1.61 (0.15), residues: 1185 sheet: -0.48 (0.42), residues: 157 loop : 0.20 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.032 0.001 TYR D 179 PHE 0.026 0.001 PHE C 227 TRP 0.006 0.001 TRP A 558 HIS 0.008 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17038) covalent geometry : angle 0.55501 / 0.29 (23020) SS BOND : bond 0.00598 / 0.31 ( 3) SS BOND : angle 2.63968 / 1.41 ( 6) hydrogen bonds : bond 0.03602 / 2.29 ( 912) hydrogen bonds : angle 4.60709 / 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 449 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 397 time to evaluate : 0.690 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: A 23 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8833 (mmmm) REVERT: A 29 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8924 (t70) REVERT: A 30 LYS cc_start: 0.8992 (tptp) cc_final: 0.8665 (tptt) REVERT: A 49 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8839 (t-90) REVERT: A 65 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7812 (mp0) REVERT: A 178 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8943 (p) REVERT: A 180 ASN cc_start: 0.8768 (m110) cc_final: 0.8412 (m110) REVERT: A 217 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8985 (mm-30) REVERT: A 250 TYR cc_start: 0.9336 (m-80) cc_final: 0.8795 (m-80) REVERT: A 263 ASP cc_start: 0.8778 (m-30) cc_final: 0.8400 (m-30) REVERT: A 274 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8189 (ttm-80) REVERT: A 286 ASP cc_start: 0.8891 (m-30) cc_final: 0.8158 (m-30) REVERT: A 290 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 317 MET cc_start: 0.9065 (mtp) cc_final: 0.8799 (mtt) REVERT: A 362 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: A 379 SER cc_start: 0.9406 (t) cc_final: 0.9073 (t) REVERT: A 420 MET cc_start: 0.9481 (mmm) cc_final: 0.9250 (mmm) REVERT: A 602 GLU cc_start: 0.8546 (tt0) cc_final: 0.8295 (tt0) REVERT: A 604 ARG cc_start: 0.8605 (mmp80) cc_final: 0.8269 (mmt-90) REVERT: A 610 LYS cc_start: 0.9112 (tppt) cc_final: 0.8886 (tppt) REVERT: A 686 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7741 (mmm-85) REVERT: B 15 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 65 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8203 (mm-30) REVERT: B 104 TYR cc_start: 0.9266 (m-80) cc_final: 0.9005 (m-80) REVERT: B 144 MET cc_start: 0.9355 (mtm) cc_final: 0.8768 (mtp) REVERT: B 150 GLN cc_start: 0.9063 (tp40) cc_final: 0.8519 (tp40) REVERT: B 266 LYS cc_start: 0.9030 (mtpp) cc_final: 0.8343 (mtpp) REVERT: B 274 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8002 (ttm170) REVERT: B 296 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8514 (mmmt) REVERT: B 333 LYS cc_start: 0.9311 (tttt) cc_final: 0.8997 (mtpp) REVERT: B 357 TYR cc_start: 0.9290 (m-10) cc_final: 0.8667 (m-80) REVERT: B 475 ASN cc_start: 0.9477 (m110) cc_final: 0.9144 (m-40) REVERT: B 586 TYR cc_start: 0.9143 (m-80) cc_final: 0.8872 (m-80) REVERT: B 602 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8084 (tt0) REVERT: B 610 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8883 (mtmm) REVERT: B 615 MET cc_start: 0.9584 (mmp) cc_final: 0.9249 (mmp) REVERT: B 662 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7930 (mpp) REVERT: B 684 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: B 686 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8022 (mtp-110) REVERT: D 91 ASN cc_start: 0.1610 (m-40) cc_final: 0.1038 (t0) REVERT: D 269 MET cc_start: 0.4062 (tpt) cc_final: 0.3562 (mpp) REVERT: E 34 MET cc_start: 0.8367 (ppp) cc_final: 0.8098 (ppp) REVERT: E 46 MET cc_start: 0.8627 (tpt) cc_final: 0.8119 (tpt) outliers start: 52 outliers final: 28 residues processed: 426 average time/residue: 0.1420 time to fit residues: 90.8414 Evaluate side-chains 412 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 376 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 49 HIS Chi-restraints excluded: chain A residue 178 SER 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 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 LEU 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 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 584 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN B 191 GLN B 239 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.187982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114728 restraints weight = 26450.300| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.13 r_work: 0.2960 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 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 (15 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17041 Z= 0.147 Angle : 0.579 15.690 23026 Z= 0.300 Chirality : 0.043 0.258 2464 Planarity : 0.003 0.044 2931 Dihedral : 8.177 137.607 2375 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.68 % Allowed : 20.07 % Favored : 77.25 % 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: 1.33 (0.19), residues: 2012 helix: 1.55 (0.15), residues: 1185 sheet: -0.53 (0.42), residues: 157 loop : 0.18 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.019 0.001 TYR C 204 PHE 0.036 0.001 PHE C 227 TRP 0.008 0.001 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (17038) covalent geometry : angle 0.57681 / 0.30 (23020) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 3.09601 / 1.64 ( 6) hydrogen bonds : bond 0.03645 / 2.32 ( 912) hydrogen bonds : angle 4.62016 / 3.19 ( 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 447 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 399 time to evaluate : 0.672 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: A 23 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8847 (mmmm) REVERT: A 29 ASP cc_start: 0.9313 (t0) cc_final: 0.8969 (t70) REVERT: A 30 LYS cc_start: 0.8948 (tptp) cc_final: 0.8599 (tptt) REVERT: A 49 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8795 (t-90) REVERT: A 65 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 178 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 217 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9041 (mm-30) REVERT: A 250 TYR cc_start: 0.9329 (m-80) cc_final: 0.8822 (m-80) REVERT: A 263 ASP cc_start: 0.8779 (m-30) cc_final: 0.8388 (m-30) REVERT: A 274 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8273 (ttm-80) REVERT: A 286 ASP cc_start: 0.8900 (m-30) cc_final: 0.8128 (m-30) REVERT: A 290 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 317 MET cc_start: 0.9045 (mtp) cc_final: 0.8735 (mtt) REVERT: A 362 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: A 420 MET cc_start: 0.9437 (mmm) cc_final: 0.9205 (mmm) REVERT: A 458 MET cc_start: 0.9128 (mmm) cc_final: 0.8872 (mmt) REVERT: A 604 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8279 (mmt-90) REVERT: A 645 GLN cc_start: 0.9197 (tp40) cc_final: 0.8953 (tp40) REVERT: A 662 MET cc_start: 0.8985 (ptp) cc_final: 0.8541 (ptp) REVERT: A 686 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7783 (mmm-85) REVERT: B 15 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8662 (mm-30) REVERT: B 44 ASN cc_start: 0.9197 (m110) cc_final: 0.8728 (m-40) REVERT: B 106 LEU cc_start: 0.9309 (tp) cc_final: 0.9105 (tp) REVERT: B 144 MET cc_start: 0.9320 (mtm) cc_final: 0.8782 (mtp) REVERT: B 150 GLN cc_start: 0.9091 (tp40) cc_final: 0.8344 (tp40) REVERT: B 228 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8951 (mtmm) REVERT: B 235 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8827 (ttm110) REVERT: B 266 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8322 (mtpp) REVERT: B 274 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8005 (ttm170) REVERT: B 296 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8548 (mmmt) REVERT: B 333 LYS cc_start: 0.9310 (tttt) cc_final: 0.8995 (mtpp) REVERT: B 357 TYR cc_start: 0.9269 (m-10) cc_final: 0.8708 (m-80) REVERT: B 416 ILE cc_start: 0.8920 (mm) cc_final: 0.8604 (mm) REVERT: B 475 ASN cc_start: 0.9469 (m110) cc_final: 0.9115 (m-40) REVERT: B 515 ASP cc_start: 0.9049 (m-30) cc_final: 0.8757 (m-30) REVERT: B 586 TYR cc_start: 0.9137 (m-80) cc_final: 0.8879 (m-80) REVERT: B 602 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8151 (tt0) REVERT: B 610 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8935 (mtmm) REVERT: B 662 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7931 (mpp) REVERT: B 684 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7305 (m-10) REVERT: B 686 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8111 (mtp-110) REVERT: C 50 ASN cc_start: 0.5748 (p0) cc_final: 0.5511 (m-40) REVERT: D 91 ASN cc_start: 0.1200 (m-40) cc_final: 0.0700 (t0) REVERT: D 195 LEU cc_start: 0.6220 (pp) cc_final: 0.5670 (mt) REVERT: D 269 MET cc_start: 0.4052 (tpt) cc_final: 0.3680 (mpp) REVERT: D 270 ASN cc_start: 0.3522 (m110) cc_final: 0.2875 (t0) REVERT: E 34 MET cc_start: 0.8499 (ppp) cc_final: 0.8295 (ppp) REVERT: E 46 MET cc_start: 0.8710 (tpt) cc_final: 0.8172 (tpt) outliers start: 48 outliers final: 32 residues processed: 426 average time/residue: 0.1352 time to fit residues: 87.1211 Evaluate side-chains 416 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 377 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 157 LEU Chi-restraints excluded: chain A residue 178 SER 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 385 VAL 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 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU 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 413 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 584 ILE 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 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: 0.5980 chunk 115 optimal weight: 2.9990 chunk 152 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN D 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.184757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106080 restraints weight = 27078.334| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.46 r_work: 0.2885 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17041 Z= 0.244 Angle : 0.635 14.542 23026 Z= 0.329 Chirality : 0.045 0.316 2464 Planarity : 0.004 0.042 2931 Dihedral : 8.274 139.296 2373 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.02 % Allowed : 20.68 % Favored : 76.30 % 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: 1.23 (0.19), residues: 2012 helix: 1.48 (0.15), residues: 1186 sheet: -0.55 (0.42), residues: 157 loop : 0.12 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 184 TYR 0.059 0.002 TYR D 179 PHE 0.039 0.002 PHE C 227 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 0.00552 / 0.24 (17038) covalent geometry : angle 0.63258 / 0.33 (23020) SS BOND : bond 0.00331 / 0.17 ( 3) SS BOND : angle 3.39041 / 1.81 ( 6) hydrogen bonds : bond 0.03800 / 2.41 ( 912) hydrogen bonds : angle 4.72420 / 3.27 ( 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 413 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 0.707 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: 0.9055 (OUTLIER) cc_final: 0.8810 (mmmm) REVERT: A 49 HIS cc_start: 0.9135 (OUTLIER) cc_final: 0.8834 (t-90) REVERT: A 65 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7990 (mp0) REVERT: A 217 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9087 (mm-30) REVERT: A 250 TYR cc_start: 0.9382 (m-80) cc_final: 0.8660 (m-80) REVERT: A 263 ASP cc_start: 0.8853 (m-30) cc_final: 0.8467 (m-30) REVERT: A 274 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8047 (ttm110) REVERT: A 286 ASP cc_start: 0.8938 (m-30) cc_final: 0.8208 (m-30) REVERT: A 290 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 316 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8595 (mm-30) REVERT: A 334 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8195 (ptpp) REVERT: A 362 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 379 SER cc_start: 0.9364 (t) cc_final: 0.9006 (t) REVERT: A 420 MET cc_start: 0.9440 (mmm) cc_final: 0.9228 (mmm) REVERT: A 458 MET cc_start: 0.9212 (mmm) cc_final: 0.8987 (mmt) REVERT: A 686 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8221 (ttm-80) REVERT: B 15 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8733 (mm-30) REVERT: B 44 ASN cc_start: 0.9184 (m110) cc_final: 0.8707 (m-40) REVERT: B 106 LEU cc_start: 0.9260 (tp) cc_final: 0.9042 (tp) REVERT: B 144 MET cc_start: 0.9422 (mtm) cc_final: 0.8950 (mtp) REVERT: B 150 GLN cc_start: 0.9220 (tp40) cc_final: 0.8723 (tp-100) REVERT: B 228 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8967 (mtmm) REVERT: B 238 ASP cc_start: 0.8238 (p0) cc_final: 0.7949 (t70) REVERT: B 266 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8406 (mtpp) REVERT: B 274 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8054 (ttm170) REVERT: B 296 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8481 (mmmt) REVERT: B 333 LYS cc_start: 0.9331 (tttt) cc_final: 0.9000 (mtpp) REVERT: B 475 ASN cc_start: 0.9452 (m110) cc_final: 0.9018 (m-40) REVERT: B 515 ASP cc_start: 0.9124 (m-30) cc_final: 0.8814 (m-30) REVERT: B 570 MET cc_start: 0.8924 (ttp) cc_final: 0.8709 (ttm) REVERT: B 586 TYR cc_start: 0.9219 (m-80) cc_final: 0.8924 (m-80) REVERT: B 602 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8183 (tt0) REVERT: B 610 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8783 (mtmm) REVERT: B 612 TYR cc_start: 0.9215 (m-80) cc_final: 0.8981 (m-80) REVERT: B 662 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: B 684 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: C 269 MET cc_start: 0.5917 (tpp) cc_final: 0.5491 (ttp) REVERT: D 91 ASN cc_start: 0.1109 (m-40) cc_final: 0.0642 (t0) REVERT: D 195 LEU cc_start: 0.6230 (pp) cc_final: 0.5739 (mt) REVERT: D 269 MET cc_start: 0.4212 (tpt) cc_final: 0.3777 (mtp) REVERT: D 287 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5928 (pt) REVERT: E 46 MET cc_start: 0.8674 (tpt) cc_final: 0.8133 (tpt) REVERT: E 70 MET cc_start: 0.7301 (mtt) cc_final: 0.6093 (mpp) outliers start: 54 outliers final: 33 residues processed: 391 average time/residue: 0.1428 time to fit residues: 84.2463 Evaluate side-chains 388 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL 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 599 GLU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU 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 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 431 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE 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 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: 0.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.0010 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 191 GLN A 218 ASN A 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111488 restraints weight = 26913.000| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.44 r_work: 0.2974 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 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 (9 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17041 Z= 0.140 Angle : 0.612 15.070 23026 Z= 0.317 Chirality : 0.043 0.310 2464 Planarity : 0.004 0.052 2931 Dihedral : 8.023 137.676 2373 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.35 % Allowed : 21.63 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2012 helix: 1.41 (0.15), residues: 1196 sheet: -0.41 (0.44), residues: 153 loop : -0.01 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.024 0.001 TYR C 204 PHE 0.032 0.001 PHE C 227 TRP 0.011 0.001 TRP D 44 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17038) covalent geometry : angle 0.61038 / 0.32 (23020) SS BOND : bond 0.00343 / 0.17 ( 3) SS BOND : angle 2.60718 / 1.39 ( 6) hydrogen bonds : bond 0.03628 / 2.29 ( 912) hydrogen bonds : angle 4.71720 / 3.27 ( 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 420 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 378 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8758 (mmmm) REVERT: A 29 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8922 (t70) REVERT: A 49 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8820 (t-90) REVERT: A 65 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7932 (mp0) REVERT: A 144 MET cc_start: 0.8937 (mmm) cc_final: 0.8610 (mtp) REVERT: A 217 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9069 (mm-30) REVERT: A 250 TYR cc_start: 0.9348 (m-80) cc_final: 0.8854 (m-80) REVERT: A 274 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8103 (ttm110) REVERT: A 286 ASP cc_start: 0.8885 (m-30) cc_final: 0.8100 (m-30) REVERT: A 290 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 316 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 362 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: A 420 MET cc_start: 0.9418 (mmm) cc_final: 0.9199 (mmm) REVERT: A 447 ASN cc_start: 0.8145 (m110) cc_final: 0.7170 (m-40) REVERT: A 458 MET cc_start: 0.9126 (mmm) cc_final: 0.8870 (mmt) REVERT: A 602 GLU cc_start: 0.8686 (tt0) cc_final: 0.8145 (tt0) REVERT: A 686 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: B 15 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8690 (mm-30) REVERT: B 44 ASN cc_start: 0.9173 (m110) cc_final: 0.8719 (m-40) REVERT: B 66 GLU cc_start: 0.8425 (tp30) cc_final: 0.8218 (tp30) REVERT: B 106 LEU cc_start: 0.9244 (tp) cc_final: 0.9019 (tp) REVERT: B 144 MET cc_start: 0.9329 (mtm) cc_final: 0.8768 (mtp) REVERT: B 150 GLN cc_start: 0.9066 (tp40) cc_final: 0.8560 (tp-100) REVERT: B 228 LYS cc_start: 0.9241 (mtpt) cc_final: 0.8952 (mtmm) REVERT: B 235 ARG cc_start: 0.9083 (ttm-80) cc_final: 0.8727 (mtm-85) REVERT: B 266 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8326 (mtpt) REVERT: B 274 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: B 333 LYS cc_start: 0.9306 (tttt) cc_final: 0.8983 (mtpp) REVERT: B 357 TYR cc_start: 0.9252 (m-10) cc_final: 0.8604 (m-80) REVERT: B 415 ASN cc_start: 0.9278 (t0) cc_final: 0.8954 (t0) REVERT: B 416 ILE cc_start: 0.8996 (mm) cc_final: 0.8679 (mm) REVERT: B 466 MET cc_start: 0.9080 (ptt) cc_final: 0.8652 (ptt) REVERT: B 475 ASN cc_start: 0.9433 (m110) cc_final: 0.9035 (m-40) REVERT: B 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8782 (m-30) REVERT: B 586 TYR cc_start: 0.9107 (m-80) cc_final: 0.8889 (m-80) REVERT: B 602 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8183 (tt0) REVERT: B 610 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8913 (mtmm) REVERT: B 662 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8013 (mpp) REVERT: B 684 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: C 269 MET cc_start: 0.5790 (tpp) cc_final: 0.5400 (ptt) REVERT: D 91 ASN cc_start: 0.1320 (m-40) cc_final: 0.0908 (t0) REVERT: D 137 MET cc_start: 0.3353 (tpt) cc_final: 0.2818 (mtm) REVERT: D 195 LEU cc_start: 0.6514 (pp) cc_final: 0.6021 (mt) REVERT: D 269 MET cc_start: 0.4097 (tpt) cc_final: 0.3669 (mpp) REVERT: E 34 MET cc_start: 0.8157 (ppp) cc_final: 0.7800 (ppp) REVERT: E 46 MET cc_start: 0.8594 (tpt) cc_final: 0.8036 (tpt) REVERT: E 70 MET cc_start: 0.7701 (mtt) cc_final: 0.6620 (mpp) outliers start: 42 outliers final: 28 residues processed: 401 average time/residue: 0.1390 time to fit residues: 84.3503 Evaluate side-chains 393 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 358 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 499 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU 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 279 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE 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 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU 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: 0.6980 chunk 96 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110887 restraints weight = 26986.259| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.35 r_work: 0.2941 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 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: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17041 Z= 0.179 Angle : 0.630 14.279 23026 Z= 0.331 Chirality : 0.044 0.332 2464 Planarity : 0.004 0.043 2931 Dihedral : 7.935 138.282 2373 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 21.91 % Favored : 75.96 % 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: 1.07 (0.19), residues: 2012 helix: 1.38 (0.15), residues: 1197 sheet: -0.57 (0.42), residues: 157 loop : -0.07 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.058 0.002 TYR D 179 PHE 0.050 0.002 PHE C 109 TRP 0.008 0.001 TRP B 558 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (17038) covalent geometry : angle 0.62830 / 0.33 (23020) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 2.69258 / 1.44 ( 6) hydrogen bonds : bond 0.03657 / 2.32 ( 912) hydrogen bonds : angle 4.69835 / 3.26 ( 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 406 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 368 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8951 (t70) REVERT: A 49 HIS cc_start: 0.9136 (OUTLIER) cc_final: 0.8803 (t-90) REVERT: A 65 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7977 (mp0) REVERT: A 217 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9097 (mm-30) REVERT: A 250 TYR cc_start: 0.9361 (m-80) cc_final: 0.8801 (m-80) REVERT: A 286 ASP cc_start: 0.8939 (m-30) cc_final: 0.8152 (m-30) REVERT: A 290 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 316 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 362 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: A 385 VAL cc_start: 0.9388 (t) cc_final: 0.9166 (p) REVERT: A 402 GLU cc_start: 0.8708 (mp0) cc_final: 0.8464 (mp0) REVERT: A 420 MET cc_start: 0.9445 (mmm) cc_final: 0.9216 (mmm) REVERT: A 458 MET cc_start: 0.9170 (mmm) cc_final: 0.8904 (mmt) REVERT: A 602 GLU cc_start: 0.8740 (tt0) cc_final: 0.8343 (tt0) REVERT: A 686 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: B 15 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8694 (mm-30) REVERT: B 44 ASN cc_start: 0.9193 (m110) cc_final: 0.8726 (m-40) REVERT: B 66 GLU cc_start: 0.8447 (tp30) cc_final: 0.8176 (tp30) REVERT: B 144 MET cc_start: 0.9350 (mtm) cc_final: 0.8809 (mtp) REVERT: B 150 GLN cc_start: 0.9095 (tp40) cc_final: 0.8579 (tp-100) REVERT: B 228 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8959 (mtmm) REVERT: B 235 ARG cc_start: 0.9147 (ttm-80) cc_final: 0.8947 (ttm-80) REVERT: B 266 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8401 (mtpp) REVERT: B 274 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: B 333 LYS cc_start: 0.9304 (tttt) cc_final: 0.8971 (mtpp) REVERT: B 357 TYR cc_start: 0.9256 (m-10) cc_final: 0.8689 (m-80) REVERT: B 415 ASN cc_start: 0.9330 (t0) cc_final: 0.9003 (t0) REVERT: B 466 MET cc_start: 0.9156 (ptt) cc_final: 0.8846 (ptt) REVERT: B 475 ASN cc_start: 0.9462 (m110) cc_final: 0.9128 (m110) REVERT: B 515 ASP cc_start: 0.9131 (m-30) cc_final: 0.8800 (m-30) REVERT: B 586 TYR cc_start: 0.9131 (m-80) cc_final: 0.8906 (m-80) REVERT: B 602 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8186 (tt0) REVERT: B 610 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8897 (mtmm) REVERT: B 662 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: B 684 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: C 269 MET cc_start: 0.5711 (tpp) cc_final: 0.5347 (ptt) REVERT: D 33 GLU cc_start: 0.4615 (mp0) cc_final: 0.3731 (pt0) REVERT: D 91 ASN cc_start: 0.1216 (m-40) cc_final: 0.0803 (t0) REVERT: D 195 LEU cc_start: 0.6307 (pp) cc_final: 0.5873 (mt) REVERT: D 269 MET cc_start: 0.4255 (tpt) cc_final: 0.3854 (mpp) REVERT: E 34 MET cc_start: 0.8267 (ppp) cc_final: 0.7869 (ppp) REVERT: E 46 MET cc_start: 0.8595 (tpt) cc_final: 0.8025 (tpt) REVERT: E 70 MET cc_start: 0.7814 (mtt) cc_final: 0.6690 (mpp) outliers start: 38 outliers final: 30 residues processed: 389 average time/residue: 0.1392 time to fit residues: 82.1463 Evaluate side-chains 391 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 499 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU 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 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 425 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 584 ILE 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 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU 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 72 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.189055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112843 restraints weight = 26452.360| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.43 r_work: 0.2972 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17041 Z= 0.139 Angle : 0.632 17.862 23026 Z= 0.328 Chirality : 0.043 0.310 2464 Planarity : 0.004 0.046 2931 Dihedral : 7.792 137.895 2373 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.84 % Allowed : 22.86 % Favored : 75.29 % 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: 1.09 (0.18), residues: 2012 helix: 1.37 (0.15), residues: 1194 sheet: 0.11 (0.49), residues: 123 loop : -0.19 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.033 0.002 TYR D 179 PHE 0.031 0.001 PHE C 227 TRP 0.012 0.001 TRP C 44 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (17038) covalent geometry : angle 0.63046 / 0.33 (23020) SS BOND : bond 0.00295 / 0.15 ( 3) SS BOND : angle 2.45615 / 1.31 ( 6) hydrogen bonds : bond 0.03574 / 2.25 ( 912) hydrogen bonds : angle 4.69146 / 3.26 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.83 seconds wall clock time: 93 minutes 1.70 seconds (5581.70 seconds total)