Starting phenix.real_space_refine on Thu Aug 6 17:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.map" model { file = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2026/9by0_45016.cif" } resolution = 4.19 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 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.95, per 1000 atoms: 0.24 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 137.904, 143.988, 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: 1.53 Conformation dependent library (CDL) restraints added in 730.8 milliseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.260A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.787A 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: 3.525A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.527A 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: 4.667A 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: 4.231A 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: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.035A 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: 3.633A 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: 4.600A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 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: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.273A 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: 6.021A 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: 6.474A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.908A 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: 8.242A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A 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: 6.588A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.817A 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: 3.879A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.878A 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: 8.264A 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: 6.467A 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: 3.23 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5051 1.34 - 1.46: 3090 1.46 - 1.58: 8708 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17038 Sorted by residual: bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " ideal model delta sigma weight residual 1.748 1.611 0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+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 1.16e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 22843 3.64 - 7.28: 160 7.28 - 10.92: 15 10.92 - 14.56: 1 14.56 - 18.20: 1 Bond angle restraints: 23020 Sorted by residual: angle pdb=" CA VAL E 69 " pdb=" C VAL E 69 " pdb=" N MET E 70 " ideal model delta sigma weight residual 116.36 105.10 11.26 9.70e-01 1.06e+00 1.35e+02 angle pdb=" O VAL E 69 " pdb=" C VAL E 69 " pdb=" N MET E 70 " ideal model delta sigma weight residual 122.66 133.31 -10.65 1.15e+00 7.56e-01 8.58e+01 angle pdb=" C VAL E 69 " pdb=" N MET E 70 " pdb=" CA MET E 70 " ideal model delta sigma weight residual 121.64 139.84 -18.20 2.13e+00 2.20e-01 7.30e+01 angle pdb=" N PHE B 624 " pdb=" CA PHE B 624 " pdb=" C PHE B 624 " ideal model delta sigma weight residual 113.01 119.15 -6.14 1.20e+00 6.94e-01 2.62e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.15: 9484 26.15 - 52.30: 699 52.30 - 78.45: 105 78.45 - 104.60: 14 104.60 - 130.75: 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 -170.27 84.27 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" C PHE B 624 " pdb=" N PHE B 624 " pdb=" CA PHE B 624 " pdb=" CB PHE B 624 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+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 -103.73 130.75 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2392 0.145 - 0.289: 67 0.289 - 0.433: 3 0.433 - 0.578: 1 0.578 - 0.722: 1 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PHE B 624 " pdb=" N PHE B 624 " pdb=" C PHE B 624 " pdb=" CB PHE B 624 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+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 4.61e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 624 " -0.084 2.00e-02 2.50e+03 5.98e-02 6.27e+01 pdb=" CG PHE B 624 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE B 624 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE B 624 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 624 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE B 624 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 624 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.68e-02 3.39e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.040 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 ASP E 58 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 126 2.51 - 3.11: 12015 3.11 - 3.70: 27825 3.70 - 4.30: 42565 4.30 - 4.90: 68561 Nonbonded interactions: 151092 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 151087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.370 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 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= 0.430 Angle : 0.880 18.197 23026 Z= 0.534 Chirality : 0.061 0.722 2464 Planarity : 0.004 0.060 2931 Dihedral : 17.508 130.755 6447 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 16.27 % Favored : 82.34 % Cbeta Deviations : 0.21 % 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: 0.56 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.31 (0.37), residues: 179 loop : 0.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.029 0.002 TYR E 67 PHE 0.120 0.003 PHE B 624 TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.36 (17038) covalent geometry : angle 0.87502 / 0.53 (23020) SS BOND : bond 0.36331 / 13.46 ( 3) SS BOND : angle 6.07971 / 3.50 ( 6) hydrogen bonds : bond 0.16741 / 11.21 ( 912) hydrogen bonds : angle 6.70349 / 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 968 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 943 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.8665 (t) cc_final: 0.8421 (p) REVERT: A 68 PHE cc_start: 0.7989 (p90) cc_final: 0.7656 (p90) REVERT: A 171 PHE cc_start: 0.8288 (m-80) cc_final: 0.7965 (m-80) REVERT: A 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8666 (t0) REVERT: A 367 VAL cc_start: 0.8707 (m) cc_final: 0.8305 (p) REVERT: A 378 PHE cc_start: 0.8293 (p90) cc_final: 0.7922 (p90) REVERT: A 483 GLU cc_start: 0.8151 (mp0) cc_final: 0.7913 (mp0) REVERT: A 655 THR cc_start: 0.9457 (m) cc_final: 0.9184 (t) REVERT: B 17 MET cc_start: 0.7011 (mmm) cc_final: 0.6211 (mmm) REVERT: B 41 ILE cc_start: 0.8798 (mm) cc_final: 0.8315 (mt) REVERT: B 46 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 51 LEU cc_start: 0.7905 (tp) cc_final: 0.7647 (tp) REVERT: B 127 LEU cc_start: 0.9293 (mt) cc_final: 0.9057 (mt) REVERT: B 129 PHE cc_start: 0.7800 (m-10) cc_final: 0.7475 (m-80) REVERT: B 177 ASP cc_start: 0.8336 (t0) cc_final: 0.7996 (t0) REVERT: B 204 SER cc_start: 0.8620 (m) cc_final: 0.8383 (t) REVERT: B 230 LEU cc_start: 0.9308 (mt) cc_final: 0.9078 (mt) REVERT: B 315 ASP cc_start: 0.8578 (p0) cc_final: 0.8274 (t0) REVERT: B 317 MET cc_start: 0.8077 (mtp) cc_final: 0.7842 (mtt) REVERT: B 322 MET cc_start: 0.7356 (mmm) cc_final: 0.6943 (mmm) REVERT: B 349 LEU cc_start: 0.8462 (mt) cc_final: 0.8147 (mp) REVERT: B 364 VAL cc_start: 0.8818 (t) cc_final: 0.8604 (t) REVERT: B 384 GLU cc_start: 0.8215 (pp20) cc_final: 0.7611 (pm20) REVERT: B 385 VAL cc_start: 0.8660 (t) cc_final: 0.8388 (t) REVERT: B 500 ILE cc_start: 0.9354 (mt) cc_final: 0.8771 (mt) REVERT: B 531 TYR cc_start: 0.6004 (m-80) cc_final: 0.5677 (m-80) REVERT: B 550 MET cc_start: 0.7101 (mtm) cc_final: 0.6594 (mtp) REVERT: B 574 TYR cc_start: 0.8035 (m-80) cc_final: 0.7823 (m-80) REVERT: B 576 LEU cc_start: 0.8710 (mt) cc_final: 0.8321 (mt) REVERT: B 626 TYR cc_start: 0.6498 (m-80) cc_final: 0.6084 (m-80) REVERT: B 644 ILE cc_start: 0.8828 (mt) cc_final: 0.8597 (mt) REVERT: B 687 THR cc_start: 0.7230 (p) cc_final: 0.6962 (p) REVERT: C 89 VAL cc_start: 0.6220 (t) cc_final: 0.5271 (t) REVERT: C 101 HIS cc_start: 0.5472 (m170) cc_final: 0.4817 (m-70) REVERT: C 131 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6054 (tp) REVERT: C 153 LEU cc_start: 0.7009 (tp) cc_final: 0.6712 (tp) REVERT: C 163 LEU cc_start: 0.6153 (tt) cc_final: 0.5806 (tp) REVERT: C 268 LEU cc_start: 0.4343 (mt) cc_final: 0.4035 (mt) REVERT: D 185 MET cc_start: 0.6867 (mmm) cc_final: 0.6543 (tpp) REVERT: D 265 ASN cc_start: 0.4744 (m-40) cc_final: 0.4463 (m110) REVERT: E 25 TRP cc_start: 0.8230 (p-90) cc_final: 0.7939 (p-90) REVERT: E 78 LEU cc_start: 0.6579 (mp) cc_final: 0.5540 (tt) outliers start: 25 outliers final: 4 residues processed: 948 average time/residue: 0.1472 time to fit residues: 206.9827 Evaluate side-chains 648 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 642 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 44 ASN B 61 ASN B 109 ASN B 191 GLN B 304 HIS B 320 ASN B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 216 GLN C 263 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094534 restraints weight = 41348.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098249 restraints weight = 21362.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100606 restraints weight = 13504.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102210 restraints weight = 9583.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103218 restraints weight = 7397.992| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17041 Z= 0.200 Angle : 0.689 15.029 23026 Z= 0.364 Chirality : 0.045 0.239 2464 Planarity : 0.004 0.046 2931 Dihedral : 9.021 136.596 2373 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 2.96 % Favored : 96.81 % 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: 1.23 (0.18), residues: 2012 helix: 1.25 (0.15), residues: 1155 sheet: -0.27 (0.38), residues: 163 loop : 0.59 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 235 TYR 0.035 0.002 TYR C 174 PHE 0.029 0.002 PHE C 168 TRP 0.022 0.002 TRP B 623 HIS 0.009 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (17038) covalent geometry : angle 0.67480 / 0.36 (23020) SS BOND : bond 0.02495 / 1.19 ( 3) SS BOND : angle 8.49854 / 4.41 ( 6) hydrogen bonds : bond 0.04824 / 3.14 ( 912) hydrogen bonds : angle 5.12412 / 3.54 ( 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 750 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 746 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9537 (tp) cc_final: 0.9322 (tp) REVERT: A 119 GLU cc_start: 0.8388 (mp0) cc_final: 0.8109 (mm-30) REVERT: A 147 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8044 (tp40) REVERT: A 195 LEU cc_start: 0.9371 (mt) cc_final: 0.9125 (mt) REVERT: A 223 VAL cc_start: 0.9470 (m) cc_final: 0.9175 (p) REVERT: A 227 MET cc_start: 0.9344 (mtm) cc_final: 0.9108 (mtm) REVERT: A 335 GLU cc_start: 0.8143 (pm20) cc_final: 0.7917 (pm20) REVERT: A 338 ASN cc_start: 0.9539 (t0) cc_final: 0.7909 (t0) REVERT: A 341 LYS cc_start: 0.9682 (mmtp) cc_final: 0.9375 (mmtp) REVERT: A 346 LEU cc_start: 0.9520 (mt) cc_final: 0.9305 (mt) REVERT: A 367 VAL cc_start: 0.9557 (m) cc_final: 0.9287 (p) REVERT: A 403 ILE cc_start: 0.9170 (mp) cc_final: 0.8902 (mp) REVERT: A 420 MET cc_start: 0.8862 (mmm) cc_final: 0.8657 (mmm) REVERT: A 421 GLU cc_start: 0.8246 (pp20) cc_final: 0.7865 (pp20) REVERT: A 453 ARG cc_start: 0.9180 (ttt-90) cc_final: 0.8955 (ttt180) REVERT: A 466 MET cc_start: 0.8062 (ptt) cc_final: 0.7720 (ptt) REVERT: A 475 ASN cc_start: 0.8299 (m110) cc_final: 0.7853 (m110) REVERT: A 509 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8414 (tm-30) REVERT: A 518 GLU cc_start: 0.8872 (pp20) cc_final: 0.8533 (pp20) REVERT: A 528 PHE cc_start: 0.8309 (m-10) cc_final: 0.7960 (m-80) REVERT: A 558 TRP cc_start: 0.8884 (m100) cc_final: 0.8540 (m100) REVERT: A 615 MET cc_start: 0.8906 (mmm) cc_final: 0.8578 (mmm) REVERT: A 639 ASP cc_start: 0.8895 (m-30) cc_final: 0.8591 (m-30) REVERT: A 658 LEU cc_start: 0.9588 (mp) cc_final: 0.9343 (mp) REVERT: B 18 ILE cc_start: 0.9378 (mm) cc_final: 0.8781 (mm) REVERT: B 127 LEU cc_start: 0.9787 (mt) cc_final: 0.9520 (mm) REVERT: B 135 GLU cc_start: 0.9157 (mp0) cc_final: 0.8821 (pm20) REVERT: B 147 GLN cc_start: 0.9040 (mt0) cc_final: 0.8577 (mt0) REVERT: B 156 PHE cc_start: 0.9261 (t80) cc_final: 0.9001 (t80) REVERT: B 186 ILE cc_start: 0.9662 (mt) cc_final: 0.9101 (mt) REVERT: B 190 MET cc_start: 0.9339 (mtm) cc_final: 0.8854 (mtm) REVERT: B 227 MET cc_start: 0.9163 (mtp) cc_final: 0.8918 (mtp) REVERT: B 256 ARG cc_start: 0.8453 (tmt170) cc_final: 0.8153 (tpt90) REVERT: B 286 ASP cc_start: 0.8408 (m-30) cc_final: 0.8130 (m-30) REVERT: B 312 GLN cc_start: 0.8777 (mt0) cc_final: 0.8419 (mt0) REVERT: B 316 GLU cc_start: 0.9341 (tt0) cc_final: 0.8825 (tt0) REVERT: B 348 MET cc_start: 0.9025 (ppp) cc_final: 0.8446 (ppp) REVERT: B 349 LEU cc_start: 0.9388 (mt) cc_final: 0.8937 (mt) REVERT: B 370 ASN cc_start: 0.9304 (m-40) cc_final: 0.8721 (m110) REVERT: B 375 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8403 (mmmm) REVERT: B 378 PHE cc_start: 0.8917 (p90) cc_final: 0.8688 (p90) REVERT: B 402 GLU cc_start: 0.8044 (mp0) cc_final: 0.7665 (mp0) REVERT: B 475 ASN cc_start: 0.9014 (m110) cc_final: 0.8714 (m110) REVERT: B 515 ASP cc_start: 0.8921 (m-30) cc_final: 0.8470 (p0) REVERT: B 546 LEU cc_start: 0.9406 (mm) cc_final: 0.9082 (mp) REVERT: B 558 TRP cc_start: 0.8746 (m100) cc_final: 0.8372 (m100) REVERT: B 574 TYR cc_start: 0.8259 (m-80) cc_final: 0.7999 (m-80) REVERT: B 586 TYR cc_start: 0.9000 (m-80) cc_final: 0.8604 (m-80) REVERT: B 634 MET cc_start: 0.8028 (mmp) cc_final: 0.7722 (mmt) REVERT: B 656 LEU cc_start: 0.9295 (mt) cc_final: 0.9009 (mt) REVERT: C 21 PHE cc_start: 0.9026 (m-80) cc_final: 0.8597 (m-80) REVERT: C 23 ASN cc_start: 0.9710 (m-40) cc_final: 0.9457 (m-40) REVERT: C 74 MET cc_start: 0.9402 (mpp) cc_final: 0.9083 (mpp) REVERT: C 154 PHE cc_start: 0.9218 (t80) cc_final: 0.8762 (t80) REVERT: C 157 MET cc_start: 0.9374 (mtm) cc_final: 0.8933 (ptt) REVERT: C 163 LEU cc_start: 0.9129 (tt) cc_final: 0.8754 (tp) REVERT: C 174 TYR cc_start: 0.8826 (t80) cc_final: 0.7672 (t80) REVERT: C 212 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7942 (mm) REVERT: C 231 LEU cc_start: 0.8829 (tp) cc_final: 0.8504 (tp) REVERT: C 233 ASN cc_start: 0.9329 (m-40) cc_final: 0.9120 (m-40) REVERT: C 285 ILE cc_start: 0.6735 (tp) cc_final: 0.6245 (tt) REVERT: D 16 ASP cc_start: 0.6718 (t0) cc_final: 0.6451 (t0) REVERT: D 109 PHE cc_start: 0.8697 (m-10) cc_final: 0.8422 (m-80) REVERT: D 115 THR cc_start: 0.8456 (m) cc_final: 0.8224 (p) REVERT: D 119 ASN cc_start: 0.8493 (m110) cc_final: 0.8139 (m-40) REVERT: D 128 ASN cc_start: 0.8959 (t0) cc_final: 0.8047 (t0) REVERT: D 133 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7788 (tptp) REVERT: E 25 TRP cc_start: 0.8184 (p-90) cc_final: 0.7757 (p-90) REVERT: E 46 MET cc_start: 0.8040 (tpp) cc_final: 0.7658 (tpt) REVERT: E 70 MET cc_start: 0.8163 (mmp) cc_final: 0.7646 (mpp) outliers start: 4 outliers final: 1 residues processed: 747 average time/residue: 0.1348 time to fit residues: 153.5823 Evaluate side-chains 598 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 596 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 25 GLN B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096150 restraints weight = 42756.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099555 restraints weight = 23094.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101789 restraints weight = 14826.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103214 restraints weight = 10584.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104358 restraints weight = 8329.021| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17041 Z= 0.165 Angle : 0.605 13.705 23026 Z= 0.320 Chirality : 0.043 0.244 2464 Planarity : 0.004 0.047 2931 Dihedral : 8.705 136.178 2373 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 1.21 (0.18), residues: 2012 helix: 1.31 (0.15), residues: 1154 sheet: -0.19 (0.39), residues: 167 loop : 0.38 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 225 TYR 0.029 0.002 TYR C 174 PHE 0.031 0.002 PHE C 166 TRP 0.011 0.001 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (17038) covalent geometry : angle 0.60408 / 0.32 (23020) SS BOND : bond 0.00533 / 0.27 ( 3) SS BOND : angle 2.23358 / 1.20 ( 6) hydrogen bonds : bond 0.04231 / 2.75 ( 912) hydrogen bonds : angle 4.86185 / 3.33 ( 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 735 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 735 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9092 (mp0) cc_final: 0.8875 (mm-30) REVERT: A 158 ASN cc_start: 0.8848 (m-40) cc_final: 0.8630 (m110) REVERT: A 209 LYS cc_start: 0.9170 (tttm) cc_final: 0.8905 (tttm) REVERT: A 223 VAL cc_start: 0.9489 (m) cc_final: 0.9136 (p) REVERT: A 254 PHE cc_start: 0.8760 (m-80) cc_final: 0.8342 (m-80) REVERT: A 367 VAL cc_start: 0.9562 (m) cc_final: 0.9303 (p) REVERT: A 390 GLN cc_start: 0.8630 (mt0) cc_final: 0.8316 (mt0) REVERT: A 403 ILE cc_start: 0.9240 (mp) cc_final: 0.8797 (mp) REVERT: A 417 LEU cc_start: 0.9363 (tp) cc_final: 0.9140 (tp) REVERT: A 420 MET cc_start: 0.8963 (mmm) cc_final: 0.8740 (mmm) REVERT: A 421 GLU cc_start: 0.8308 (pp20) cc_final: 0.7973 (pp20) REVERT: A 453 ARG cc_start: 0.9186 (ttt-90) cc_final: 0.8941 (ttt-90) REVERT: A 475 ASN cc_start: 0.8391 (m110) cc_final: 0.7958 (m110) REVERT: A 501 GLN cc_start: 0.9294 (tt0) cc_final: 0.8819 (tm-30) REVERT: A 505 GLU cc_start: 0.8633 (pt0) cc_final: 0.8187 (pt0) REVERT: A 509 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 558 TRP cc_start: 0.8966 (m100) cc_final: 0.8657 (m100) REVERT: A 615 MET cc_start: 0.9070 (mmm) cc_final: 0.8636 (mmm) REVERT: A 639 ASP cc_start: 0.8838 (m-30) cc_final: 0.8609 (m-30) REVERT: A 645 GLN cc_start: 0.8587 (tp40) cc_final: 0.8339 (tp40) REVERT: A 650 GLN cc_start: 0.7941 (mt0) cc_final: 0.7573 (mt0) REVERT: A 658 LEU cc_start: 0.9581 (mp) cc_final: 0.9302 (mp) REVERT: A 686 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7341 (mtp-110) REVERT: B 18 ILE cc_start: 0.9445 (mm) cc_final: 0.8903 (pt) REVERT: B 30 LYS cc_start: 0.9116 (tptt) cc_final: 0.8797 (tptp) REVERT: B 40 TYR cc_start: 0.9313 (t80) cc_final: 0.9082 (t80) REVERT: B 99 LYS cc_start: 0.9427 (tptm) cc_final: 0.9070 (tptp) REVERT: B 100 PHE cc_start: 0.9468 (t80) cc_final: 0.9240 (t80) REVERT: B 127 LEU cc_start: 0.9792 (mt) cc_final: 0.9504 (mm) REVERT: B 129 PHE cc_start: 0.9139 (m-80) cc_final: 0.8916 (m-80) REVERT: B 135 GLU cc_start: 0.8983 (mp0) cc_final: 0.8779 (pm20) REVERT: B 147 GLN cc_start: 0.8942 (mt0) cc_final: 0.8539 (mt0) REVERT: B 150 GLN cc_start: 0.9357 (tp40) cc_final: 0.8653 (tp-100) REVERT: B 184 ARG cc_start: 0.9546 (tpp80) cc_final: 0.8907 (tpp80) REVERT: B 186 ILE cc_start: 0.9521 (mt) cc_final: 0.9233 (mt) REVERT: B 190 MET cc_start: 0.9273 (mtm) cc_final: 0.9004 (mtm) REVERT: B 232 ASN cc_start: 0.9111 (m-40) cc_final: 0.8878 (m110) REVERT: B 252 ASN cc_start: 0.9414 (t0) cc_final: 0.8985 (t0) REVERT: B 256 ARG cc_start: 0.8348 (tmt170) cc_final: 0.7971 (tpt90) REVERT: B 286 ASP cc_start: 0.8264 (m-30) cc_final: 0.7966 (m-30) REVERT: B 335 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 348 MET cc_start: 0.8896 (ppp) cc_final: 0.8406 (ppp) REVERT: B 349 LEU cc_start: 0.9348 (mt) cc_final: 0.8787 (mt) REVERT: B 361 GLN cc_start: 0.8187 (tm130) cc_final: 0.7797 (tp40) REVERT: B 370 ASN cc_start: 0.9467 (m-40) cc_final: 0.9082 (m110) REVERT: B 375 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8469 (mmmm) REVERT: B 378 PHE cc_start: 0.8964 (p90) cc_final: 0.8656 (p90) REVERT: B 402 GLU cc_start: 0.8054 (mp0) cc_final: 0.7656 (mp0) REVERT: B 437 THR cc_start: 0.9608 (m) cc_final: 0.9265 (m) REVERT: B 475 ASN cc_start: 0.8969 (m-40) cc_final: 0.8636 (m110) REVERT: B 490 THR cc_start: 0.9275 (m) cc_final: 0.8842 (p) REVERT: B 493 MET cc_start: 0.9329 (tmm) cc_final: 0.8709 (tmm) REVERT: B 510 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9238 (mmtp) REVERT: B 515 ASP cc_start: 0.8908 (m-30) cc_final: 0.8545 (p0) REVERT: B 526 GLU cc_start: 0.8812 (mp0) cc_final: 0.8610 (mp0) REVERT: B 528 PHE cc_start: 0.9106 (m-80) cc_final: 0.8808 (m-80) REVERT: B 574 TYR cc_start: 0.8383 (m-80) cc_final: 0.8181 (m-80) REVERT: B 586 TYR cc_start: 0.8981 (m-80) cc_final: 0.8755 (m-80) REVERT: B 612 TYR cc_start: 0.8297 (m-80) cc_final: 0.7789 (m-80) REVERT: B 623 TRP cc_start: 0.8321 (t-100) cc_final: 0.7885 (t-100) REVERT: B 656 LEU cc_start: 0.9328 (mt) cc_final: 0.8998 (mt) REVERT: C 17 PHE cc_start: 0.8912 (p90) cc_final: 0.8212 (p90) REVERT: C 20 MET cc_start: 0.9109 (ppp) cc_final: 0.8852 (ppp) REVERT: C 21 PHE cc_start: 0.8965 (m-80) cc_final: 0.8246 (m-80) REVERT: C 56 MET cc_start: 0.0887 (ptm) cc_final: 0.0287 (ttp) REVERT: C 74 MET cc_start: 0.9389 (mpp) cc_final: 0.9060 (mpp) REVERT: C 89 VAL cc_start: 0.7720 (t) cc_final: 0.7219 (t) REVERT: C 95 MET cc_start: 0.8558 (ttp) cc_final: 0.8052 (ttp) REVERT: C 157 MET cc_start: 0.9422 (mtm) cc_final: 0.9031 (ptp) REVERT: C 163 LEU cc_start: 0.9185 (tt) cc_final: 0.8807 (tp) REVERT: C 169 TYR cc_start: 0.8074 (m-10) cc_final: 0.7811 (m-80) REVERT: C 174 TYR cc_start: 0.8768 (t80) cc_final: 0.7319 (t80) REVERT: C 178 PHE cc_start: 0.8815 (m-10) cc_final: 0.7973 (m-10) REVERT: C 212 ILE cc_start: 0.8761 (mt) cc_final: 0.8415 (mm) REVERT: D 42 LEU cc_start: 0.9263 (mt) cc_final: 0.8909 (mp) REVERT: D 109 PHE cc_start: 0.8697 (m-10) cc_final: 0.8361 (m-80) REVERT: D 128 ASN cc_start: 0.8403 (t0) cc_final: 0.7309 (t0) REVERT: D 133 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8047 (tptp) REVERT: D 242 TYR cc_start: 0.7932 (t80) cc_final: 0.7526 (t80) REVERT: E 25 TRP cc_start: 0.8256 (p-90) cc_final: 0.7494 (p-90) REVERT: E 46 MET cc_start: 0.8245 (tpp) cc_final: 0.7995 (tpp) REVERT: E 70 MET cc_start: 0.8035 (mmp) cc_final: 0.7259 (mpp) outliers start: 0 outliers final: 0 residues processed: 735 average time/residue: 0.1322 time to fit residues: 149.0865 Evaluate side-chains 591 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 474 GLN C 28 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 91 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 = 0.3729 r_free = 0.3729 target = 0.128355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090755 restraints weight = 43420.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094194 restraints weight = 23295.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096399 restraints weight = 14752.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097801 restraints weight = 10574.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098923 restraints weight = 8372.159| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17041 Z= 0.234 Angle : 0.654 11.225 23026 Z= 0.345 Chirality : 0.044 0.286 2464 Planarity : 0.004 0.039 2931 Dihedral : 8.727 139.384 2373 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1158 sheet: -0.14 (0.40), residues: 165 loop : 0.38 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 225 TYR 0.033 0.002 TYR C 174 PHE 0.023 0.002 PHE D 154 TRP 0.019 0.002 TRP A 623 HIS 0.014 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (17038) covalent geometry : angle 0.65199 / 0.34 (23020) SS BOND : bond 0.00974 / 0.46 ( 3) SS BOND : angle 3.55460 / 1.84 ( 6) hydrogen bonds : bond 0.04238 / 2.75 ( 912) hydrogen bonds : angle 5.03153 / 3.50 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 679 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9232 (tp) cc_final: 0.8949 (tp) REVERT: A 147 GLN cc_start: 0.8528 (tp-100) cc_final: 0.7584 (tp-100) REVERT: A 162 LYS cc_start: 0.9458 (tmtt) cc_final: 0.9082 (tmmt) REVERT: A 195 LEU cc_start: 0.9377 (mt) cc_final: 0.9157 (mt) REVERT: A 250 TYR cc_start: 0.8125 (m-80) cc_final: 0.7900 (m-80) REVERT: A 286 ASP cc_start: 0.8852 (m-30) cc_final: 0.8551 (m-30) REVERT: A 301 PHE cc_start: 0.8952 (m-80) cc_final: 0.8647 (m-10) REVERT: A 322 MET cc_start: 0.8025 (mmm) cc_final: 0.7652 (mmm) REVERT: A 362 ASP cc_start: 0.8456 (m-30) cc_final: 0.8138 (m-30) REVERT: A 367 VAL cc_start: 0.9593 (m) cc_final: 0.9342 (p) REVERT: A 421 GLU cc_start: 0.8349 (pp20) cc_final: 0.8054 (pp20) REVERT: A 475 ASN cc_start: 0.8569 (m110) cc_final: 0.8319 (m110) REVERT: A 498 TYR cc_start: 0.8639 (m-80) cc_final: 0.8243 (m-80) REVERT: A 501 GLN cc_start: 0.9400 (tt0) cc_final: 0.8770 (tm-30) REVERT: A 505 GLU cc_start: 0.8590 (pt0) cc_final: 0.8066 (pt0) REVERT: A 515 ASP cc_start: 0.8887 (m-30) cc_final: 0.8548 (m-30) REVERT: A 615 MET cc_start: 0.9100 (mmm) cc_final: 0.8699 (mmm) REVERT: A 658 LEU cc_start: 0.9623 (mp) cc_final: 0.9266 (mp) REVERT: B 18 ILE cc_start: 0.9428 (mm) cc_final: 0.8766 (tp) REVERT: B 20 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8420 (mmtp) REVERT: B 27 ASP cc_start: 0.9445 (p0) cc_final: 0.9095 (p0) REVERT: B 87 LYS cc_start: 0.9147 (tppt) cc_final: 0.8489 (tptp) REVERT: B 117 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7785 (mmm-85) REVERT: B 120 ASP cc_start: 0.8679 (m-30) cc_final: 0.8135 (m-30) REVERT: B 127 LEU cc_start: 0.9812 (mt) cc_final: 0.9539 (mm) REVERT: B 129 PHE cc_start: 0.9133 (m-80) cc_final: 0.8894 (m-80) REVERT: B 147 GLN cc_start: 0.9180 (mt0) cc_final: 0.8192 (mm-40) REVERT: B 150 GLN cc_start: 0.9534 (tp40) cc_final: 0.8869 (tp-100) REVERT: B 184 ARG cc_start: 0.9502 (tpp80) cc_final: 0.8759 (tpp80) REVERT: B 190 MET cc_start: 0.9224 (mtm) cc_final: 0.9024 (mtm) REVERT: B 205 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7983 (mmmm) REVERT: B 232 ASN cc_start: 0.9136 (m-40) cc_final: 0.8936 (m110) REVERT: B 256 ARG cc_start: 0.8302 (tmt170) cc_final: 0.8066 (ttp80) REVERT: B 258 ILE cc_start: 0.9427 (tp) cc_final: 0.9206 (tp) REVERT: B 286 ASP cc_start: 0.8332 (m-30) cc_final: 0.8011 (m-30) REVERT: B 322 MET cc_start: 0.8564 (mmt) cc_final: 0.8327 (mmm) REVERT: B 348 MET cc_start: 0.8943 (ppp) cc_final: 0.8472 (ppp) REVERT: B 349 LEU cc_start: 0.9377 (mt) cc_final: 0.8663 (mt) REVERT: B 361 GLN cc_start: 0.8250 (pp30) cc_final: 0.7718 (pp30) REVERT: B 370 ASN cc_start: 0.9495 (m-40) cc_final: 0.9202 (m110) REVERT: B 375 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8479 (mmmm) REVERT: B 402 GLU cc_start: 0.8169 (mp0) cc_final: 0.7741 (mp0) REVERT: B 415 ASN cc_start: 0.9154 (t0) cc_final: 0.8792 (t0) REVERT: B 437 THR cc_start: 0.9601 (m) cc_final: 0.9276 (m) REVERT: B 475 ASN cc_start: 0.9081 (m-40) cc_final: 0.8751 (m110) REVERT: B 515 ASP cc_start: 0.8899 (m-30) cc_final: 0.8655 (p0) REVERT: B 526 GLU cc_start: 0.8825 (mp0) cc_final: 0.8575 (mp0) REVERT: B 574 TYR cc_start: 0.8453 (m-80) cc_final: 0.8100 (m-80) REVERT: B 586 TYR cc_start: 0.8960 (m-80) cc_final: 0.8682 (m-80) REVERT: B 599 GLU cc_start: 0.8733 (mp0) cc_final: 0.8410 (mp0) REVERT: B 612 TYR cc_start: 0.8096 (m-80) cc_final: 0.7618 (m-80) REVERT: B 623 TRP cc_start: 0.8380 (t-100) cc_final: 0.8157 (t-100) REVERT: B 656 LEU cc_start: 0.9274 (mt) cc_final: 0.9028 (mt) REVERT: C 17 PHE cc_start: 0.9020 (p90) cc_final: 0.8355 (p90) REVERT: C 20 MET cc_start: 0.9229 (ppp) cc_final: 0.8978 (ppp) REVERT: C 21 PHE cc_start: 0.9086 (m-80) cc_final: 0.8539 (m-80) REVERT: C 46 TYR cc_start: 0.7682 (m-80) cc_final: 0.7351 (m-80) REVERT: C 68 GLU cc_start: 0.8958 (mp0) cc_final: 0.8554 (pm20) REVERT: C 74 MET cc_start: 0.9362 (mpp) cc_final: 0.9034 (mpp) REVERT: C 89 VAL cc_start: 0.7728 (t) cc_final: 0.7202 (m) REVERT: C 95 MET cc_start: 0.8596 (ttp) cc_final: 0.7993 (ttp) REVERT: C 154 PHE cc_start: 0.9140 (t80) cc_final: 0.8883 (t80) REVERT: C 157 MET cc_start: 0.9422 (mtm) cc_final: 0.9062 (ptt) REVERT: C 163 LEU cc_start: 0.9281 (tt) cc_final: 0.8930 (tt) REVERT: C 169 TYR cc_start: 0.8365 (m-10) cc_final: 0.8113 (m-80) REVERT: C 187 SER cc_start: 0.8289 (m) cc_final: 0.8082 (p) REVERT: C 212 ILE cc_start: 0.8779 (mt) cc_final: 0.8298 (mm) REVERT: C 231 LEU cc_start: 0.9159 (mt) cc_final: 0.8847 (mt) REVERT: E 25 TRP cc_start: 0.8296 (p-90) cc_final: 0.7534 (p-90) REVERT: E 46 MET cc_start: 0.8381 (tpp) cc_final: 0.8129 (tpp) REVERT: E 60 ASN cc_start: 0.9392 (t0) cc_final: 0.9173 (t0) REVERT: E 70 MET cc_start: 0.8057 (mmp) cc_final: 0.7661 (mpp) REVERT: E 77 VAL cc_start: 0.9084 (t) cc_final: 0.8766 (t) outliers start: 2 outliers final: 1 residues processed: 679 average time/residue: 0.1336 time to fit residues: 139.1898 Evaluate side-chains 580 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 0.0010 chunk 146 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 158 ASN A 304 HIS A 365 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.139475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102297 restraints weight = 42671.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105774 restraints weight = 23039.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107871 restraints weight = 14645.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109461 restraints weight = 10615.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110411 restraints weight = 8352.122| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17041 Z= 0.130 Angle : 0.616 12.776 23026 Z= 0.322 Chirality : 0.044 0.315 2464 Planarity : 0.004 0.039 2931 Dihedral : 8.411 135.990 2373 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1146 sheet: -0.15 (0.41), residues: 165 loop : 0.37 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.035 0.002 TYR C 174 PHE 0.040 0.002 PHE D 122 TRP 0.006 0.001 TRP A 623 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17038) covalent geometry : angle 0.61061 / 0.32 (23020) SS BOND : bond 0.00535 / 0.26 ( 3) SS BOND : angle 5.11266 / 2.47 ( 6) hydrogen bonds : bond 0.03972 / 2.57 ( 912) hydrogen bonds : angle 4.92301 / 3.46 ( 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 703 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 703 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.9487 (mmtt) cc_final: 0.9216 (mmmm) REVERT: A 150 GLN cc_start: 0.8695 (tp40) cc_final: 0.8236 (tp40) REVERT: A 162 LYS cc_start: 0.9238 (tmtt) cc_final: 0.9010 (tmmt) REVERT: A 187 ASP cc_start: 0.8641 (t70) cc_final: 0.8221 (t0) REVERT: A 227 MET cc_start: 0.9217 (ptp) cc_final: 0.8959 (ptp) REVERT: A 228 LYS cc_start: 0.8987 (tptt) cc_final: 0.8588 (mptt) REVERT: A 286 ASP cc_start: 0.8834 (m-30) cc_final: 0.8582 (m-30) REVERT: A 290 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8858 (tm-30) REVERT: A 313 HIS cc_start: 0.8307 (m-70) cc_final: 0.7927 (m-70) REVERT: A 348 MET cc_start: 0.8858 (ptm) cc_final: 0.8601 (ptm) REVERT: A 362 ASP cc_start: 0.8339 (m-30) cc_final: 0.8117 (m-30) REVERT: A 367 VAL cc_start: 0.9562 (m) cc_final: 0.9316 (p) REVERT: A 390 GLN cc_start: 0.8634 (mt0) cc_final: 0.8423 (mt0) REVERT: A 418 ASN cc_start: 0.9269 (m-40) cc_final: 0.8558 (m110) REVERT: A 498 TYR cc_start: 0.8679 (m-80) cc_final: 0.8205 (m-80) REVERT: A 501 GLN cc_start: 0.9327 (tt0) cc_final: 0.8592 (tm-30) REVERT: A 505 GLU cc_start: 0.8657 (pt0) cc_final: 0.8011 (pt0) REVERT: A 515 ASP cc_start: 0.8921 (m-30) cc_final: 0.8448 (m-30) REVERT: A 613 TYR cc_start: 0.8374 (t80) cc_final: 0.7938 (t80) REVERT: A 615 MET cc_start: 0.9051 (mmm) cc_final: 0.8702 (mmm) REVERT: A 658 LEU cc_start: 0.9626 (mp) cc_final: 0.9314 (mp) REVERT: A 686 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7581 (mtp-110) REVERT: B 30 LYS cc_start: 0.9272 (tmtt) cc_final: 0.9052 (tptt) REVERT: B 87 LYS cc_start: 0.9086 (tppt) cc_final: 0.8432 (ttmt) REVERT: B 99 LYS cc_start: 0.9437 (tptm) cc_final: 0.9160 (tptm) REVERT: B 117 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7805 (mmm-85) REVERT: B 120 ASP cc_start: 0.8685 (m-30) cc_final: 0.8274 (m-30) REVERT: B 127 LEU cc_start: 0.9789 (mt) cc_final: 0.9475 (mm) REVERT: B 129 PHE cc_start: 0.9133 (m-10) cc_final: 0.8834 (m-80) REVERT: B 145 ILE cc_start: 0.9349 (tp) cc_final: 0.8979 (tp) REVERT: B 147 GLN cc_start: 0.8938 (mt0) cc_final: 0.7984 (mm-40) REVERT: B 150 GLN cc_start: 0.9556 (tp40) cc_final: 0.9288 (tp-100) REVERT: B 184 ARG cc_start: 0.9461 (tpp80) cc_final: 0.9196 (tpp80) REVERT: B 190 MET cc_start: 0.9267 (mtm) cc_final: 0.9035 (mtm) REVERT: B 228 LYS cc_start: 0.9559 (mmmt) cc_final: 0.9200 (mmmt) REVERT: B 232 ASN cc_start: 0.9116 (m-40) cc_final: 0.8673 (m110) REVERT: B 256 ARG cc_start: 0.8357 (tmt170) cc_final: 0.8086 (ttp80) REVERT: B 258 ILE cc_start: 0.9415 (tp) cc_final: 0.9200 (tp) REVERT: B 286 ASP cc_start: 0.8347 (m-30) cc_final: 0.7972 (m-30) REVERT: B 322 MET cc_start: 0.8502 (mmt) cc_final: 0.8225 (mmm) REVERT: B 335 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 348 MET cc_start: 0.8992 (ppp) cc_final: 0.8485 (ppp) REVERT: B 349 LEU cc_start: 0.9346 (mt) cc_final: 0.8611 (mt) REVERT: B 361 GLN cc_start: 0.8110 (pp30) cc_final: 0.7426 (pp30) REVERT: B 370 ASN cc_start: 0.9437 (m-40) cc_final: 0.9086 (m110) REVERT: B 375 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8522 (mmmm) REVERT: B 378 PHE cc_start: 0.8942 (p90) cc_final: 0.8580 (p90) REVERT: B 402 GLU cc_start: 0.8048 (mp0) cc_final: 0.7572 (mp0) REVERT: B 426 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8374 (mm-30) REVERT: B 437 THR cc_start: 0.9574 (m) cc_final: 0.9259 (m) REVERT: B 446 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7185 (mpt90) REVERT: B 475 ASN cc_start: 0.9082 (m-40) cc_final: 0.8793 (m110) REVERT: B 515 ASP cc_start: 0.8877 (m-30) cc_final: 0.8493 (p0) REVERT: B 526 GLU cc_start: 0.8837 (mp0) cc_final: 0.8577 (mp0) REVERT: B 570 MET cc_start: 0.8743 (tpp) cc_final: 0.8458 (tpt) REVERT: B 574 TYR cc_start: 0.8340 (m-80) cc_final: 0.7912 (m-80) REVERT: B 575 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8382 (ptp90) REVERT: B 612 TYR cc_start: 0.8144 (m-80) cc_final: 0.7686 (m-80) REVERT: B 624 PHE cc_start: 0.7856 (m-10) cc_final: 0.7611 (m-10) REVERT: B 632 MET cc_start: 0.7612 (mtm) cc_final: 0.7398 (mtp) REVERT: B 656 LEU cc_start: 0.9304 (mt) cc_final: 0.9049 (mt) REVERT: B 658 LEU cc_start: 0.8791 (mp) cc_final: 0.8589 (mp) REVERT: C 17 PHE cc_start: 0.9001 (p90) cc_final: 0.8363 (p90) REVERT: C 20 MET cc_start: 0.9296 (ppp) cc_final: 0.9032 (ppp) REVERT: C 21 PHE cc_start: 0.9023 (m-80) cc_final: 0.8461 (m-80) REVERT: C 46 TYR cc_start: 0.7666 (m-80) cc_final: 0.7325 (m-80) REVERT: C 56 MET cc_start: 0.1104 (ptm) cc_final: 0.0420 (ttp) REVERT: C 95 MET cc_start: 0.8512 (ttp) cc_final: 0.8000 (ttp) REVERT: C 154 PHE cc_start: 0.9070 (t80) cc_final: 0.8694 (t80) REVERT: C 157 MET cc_start: 0.9406 (mtm) cc_final: 0.9101 (ptt) REVERT: C 169 TYR cc_start: 0.8427 (m-10) cc_final: 0.8180 (m-80) REVERT: C 174 TYR cc_start: 0.8886 (t80) cc_final: 0.8170 (t80) REVERT: C 212 ILE cc_start: 0.8676 (mt) cc_final: 0.7918 (tp) REVERT: C 226 GLU cc_start: 0.8972 (pt0) cc_final: 0.8703 (pt0) REVERT: C 321 TYR cc_start: 0.8045 (m-80) cc_final: 0.7808 (m-80) REVERT: D 128 ASN cc_start: 0.8344 (t0) cc_final: 0.7398 (t0) REVERT: D 133 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8092 (tptp) REVERT: D 185 MET cc_start: 0.6776 (ptm) cc_final: 0.6527 (ptm) REVERT: D 242 TYR cc_start: 0.7768 (t80) cc_final: 0.7326 (t80) REVERT: E 25 TRP cc_start: 0.8097 (p-90) cc_final: 0.7470 (p-90) REVERT: E 46 MET cc_start: 0.8282 (tpp) cc_final: 0.8011 (tpp) REVERT: E 70 MET cc_start: 0.8170 (mmp) cc_final: 0.7913 (mpp) REVERT: E 93 LYS cc_start: 0.7726 (tptp) cc_final: 0.7299 (tptt) outliers start: 0 outliers final: 0 residues processed: 703 average time/residue: 0.1321 time to fit residues: 143.0358 Evaluate side-chains 580 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098744 restraints weight = 42950.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102207 restraints weight = 22666.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104479 restraints weight = 14259.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105868 restraints weight = 10226.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106899 restraints weight = 8151.377| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6493 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= 0.157 Angle : 0.626 11.879 23026 Z= 0.325 Chirality : 0.044 0.268 2464 Planarity : 0.004 0.040 2931 Dihedral : 8.350 138.312 2373 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1154 sheet: -0.29 (0.41), residues: 169 loop : 0.22 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 256 TYR 0.027 0.002 TYR C 174 PHE 0.037 0.002 PHE B 171 TRP 0.010 0.001 TRP A 623 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (17038) covalent geometry : angle 0.62274 / 0.32 (23020) SS BOND : bond 0.00486 / 0.24 ( 3) SS BOND : angle 3.95547 / 1.94 ( 6) hydrogen bonds : bond 0.03889 / 2.52 ( 912) hydrogen bonds : angle 4.96262 / 3.46 ( 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 671 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8931 (tptp) cc_final: 0.8595 (tppt) REVERT: A 113 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9229 (mmmm) REVERT: A 209 LYS cc_start: 0.9281 (tttm) cc_final: 0.9065 (tttm) REVERT: A 227 MET cc_start: 0.9292 (ptp) cc_final: 0.8981 (ptp) REVERT: A 228 LYS cc_start: 0.9026 (tptt) cc_final: 0.8558 (mptt) REVERT: A 250 TYR cc_start: 0.8152 (m-80) cc_final: 0.7769 (m-80) REVERT: A 254 PHE cc_start: 0.8728 (m-80) cc_final: 0.8360 (m-80) REVERT: A 286 ASP cc_start: 0.8813 (m-30) cc_final: 0.8599 (m-30) REVERT: A 290 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 301 PHE cc_start: 0.8826 (m-80) cc_final: 0.8611 (m-10) REVERT: A 322 MET cc_start: 0.8189 (mmm) cc_final: 0.7828 (mmm) REVERT: A 338 ASN cc_start: 0.9493 (t0) cc_final: 0.9183 (t0) REVERT: A 346 LEU cc_start: 0.9434 (mt) cc_final: 0.9226 (mt) REVERT: A 348 MET cc_start: 0.8892 (ptm) cc_final: 0.8638 (ptm) REVERT: A 362 ASP cc_start: 0.8373 (m-30) cc_final: 0.7995 (m-30) REVERT: A 367 VAL cc_start: 0.9563 (m) cc_final: 0.9335 (p) REVERT: A 390 GLN cc_start: 0.8707 (mt0) cc_final: 0.8490 (mt0) REVERT: A 417 LEU cc_start: 0.9311 (tp) cc_final: 0.8993 (tp) REVERT: A 418 ASN cc_start: 0.9022 (m-40) cc_final: 0.8597 (m-40) REVERT: A 491 PHE cc_start: 0.9526 (t80) cc_final: 0.8955 (t80) REVERT: A 498 TYR cc_start: 0.8764 (m-80) cc_final: 0.8270 (m-80) REVERT: A 501 GLN cc_start: 0.9344 (tt0) cc_final: 0.8634 (tm-30) REVERT: A 505 GLU cc_start: 0.8677 (pt0) cc_final: 0.7896 (pt0) REVERT: A 515 ASP cc_start: 0.8917 (m-30) cc_final: 0.8521 (m-30) REVERT: A 558 TRP cc_start: 0.9002 (m100) cc_final: 0.8700 (m100) REVERT: A 590 SER cc_start: 0.9552 (t) cc_final: 0.9177 (p) REVERT: A 615 MET cc_start: 0.9061 (mmm) cc_final: 0.8767 (mmm) REVERT: A 645 GLN cc_start: 0.8737 (tp40) cc_final: 0.7930 (tp40) REVERT: A 686 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7716 (mtp-110) REVERT: B 30 LYS cc_start: 0.9289 (tmtt) cc_final: 0.9055 (tptt) REVERT: B 87 LYS cc_start: 0.9096 (tppt) cc_final: 0.8482 (tptp) REVERT: B 99 LYS cc_start: 0.9450 (tptm) cc_final: 0.9250 (tptm) REVERT: B 117 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7700 (mmm-85) REVERT: B 120 ASP cc_start: 0.8678 (m-30) cc_final: 0.8264 (m-30) REVERT: B 127 LEU cc_start: 0.9777 (mt) cc_final: 0.9457 (mm) REVERT: B 129 PHE cc_start: 0.9166 (m-10) cc_final: 0.8902 (m-80) REVERT: B 147 GLN cc_start: 0.9110 (mt0) cc_final: 0.8045 (mm-40) REVERT: B 150 GLN cc_start: 0.9564 (tp40) cc_final: 0.9352 (tp-100) REVERT: B 184 ARG cc_start: 0.9468 (tpp80) cc_final: 0.9214 (tpp80) REVERT: B 186 ILE cc_start: 0.9565 (mt) cc_final: 0.9307 (mt) REVERT: B 190 MET cc_start: 0.9248 (mtm) cc_final: 0.9005 (mtm) REVERT: B 232 ASN cc_start: 0.9052 (m-40) cc_final: 0.8754 (m110) REVERT: B 256 ARG cc_start: 0.8326 (tmt170) cc_final: 0.8056 (ttp80) REVERT: B 258 ILE cc_start: 0.9404 (tp) cc_final: 0.9187 (tp) REVERT: B 286 ASP cc_start: 0.8497 (m-30) cc_final: 0.8286 (m-30) REVERT: B 322 MET cc_start: 0.8472 (mmt) cc_final: 0.8212 (mmm) REVERT: B 348 MET cc_start: 0.8965 (ppp) cc_final: 0.8431 (ppp) REVERT: B 349 LEU cc_start: 0.9350 (mt) cc_final: 0.8658 (mt) REVERT: B 361 GLN cc_start: 0.7948 (pp30) cc_final: 0.7370 (pp30) REVERT: B 370 ASN cc_start: 0.9513 (m-40) cc_final: 0.9146 (m110) REVERT: B 375 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8475 (mmmm) REVERT: B 378 PHE cc_start: 0.8964 (p90) cc_final: 0.8529 (p90) REVERT: B 415 ASN cc_start: 0.8625 (t0) cc_final: 0.8310 (t0) REVERT: B 437 THR cc_start: 0.9594 (m) cc_final: 0.9231 (m) REVERT: B 444 ASP cc_start: 0.7970 (p0) cc_final: 0.7725 (p0) REVERT: B 475 ASN cc_start: 0.9189 (m-40) cc_final: 0.8837 (m110) REVERT: B 515 ASP cc_start: 0.8889 (m-30) cc_final: 0.8607 (p0) REVERT: B 526 GLU cc_start: 0.8831 (mp0) cc_final: 0.8629 (mp0) REVERT: B 575 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8498 (ptp90) REVERT: B 586 TYR cc_start: 0.9101 (m-80) cc_final: 0.8841 (m-80) REVERT: B 599 GLU cc_start: 0.8993 (pm20) cc_final: 0.8746 (pm20) REVERT: B 612 TYR cc_start: 0.8412 (m-80) cc_final: 0.8108 (m-80) REVERT: B 656 LEU cc_start: 0.9297 (mt) cc_final: 0.9083 (mt) REVERT: B 658 LEU cc_start: 0.8889 (mp) cc_final: 0.8596 (mp) REVERT: C 17 PHE cc_start: 0.9014 (p90) cc_final: 0.8342 (p90) REVERT: C 20 MET cc_start: 0.9290 (ppp) cc_final: 0.9013 (ppp) REVERT: C 21 PHE cc_start: 0.9041 (m-80) cc_final: 0.8485 (m-80) REVERT: C 46 TYR cc_start: 0.7720 (m-80) cc_final: 0.7366 (m-80) REVERT: C 56 MET cc_start: 0.1100 (ptm) cc_final: 0.0291 (ttp) REVERT: C 68 GLU cc_start: 0.8949 (mp0) cc_final: 0.8723 (pm20) REVERT: C 74 MET cc_start: 0.9301 (mpp) cc_final: 0.9079 (mpp) REVERT: C 89 VAL cc_start: 0.7669 (t) cc_final: 0.7149 (m) REVERT: C 95 MET cc_start: 0.8335 (ttp) cc_final: 0.7515 (ttp) REVERT: C 169 TYR cc_start: 0.8424 (m-80) cc_final: 0.8177 (m-80) REVERT: C 174 TYR cc_start: 0.8900 (t80) cc_final: 0.8095 (t80) REVERT: C 178 PHE cc_start: 0.9027 (m-10) cc_final: 0.8784 (m-10) REVERT: C 277 PHE cc_start: 0.6824 (m-10) cc_final: 0.6484 (m-80) REVERT: D 92 PHE cc_start: 0.6867 (t80) cc_final: 0.6507 (t80) REVERT: D 185 MET cc_start: 0.6823 (ptm) cc_final: 0.6558 (ptm) REVERT: E 25 TRP cc_start: 0.8132 (p-90) cc_final: 0.7497 (p-90) REVERT: E 46 MET cc_start: 0.8241 (tpp) cc_final: 0.7918 (tpp) REVERT: E 60 ASN cc_start: 0.9400 (t0) cc_final: 0.9190 (t0) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.1356 time to fit residues: 139.1391 Evaluate side-chains 569 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 320 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 132 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.137813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101341 restraints weight = 42479.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104655 restraints weight = 22750.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106879 restraints weight = 14641.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108277 restraints weight = 10482.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109388 restraints weight = 8318.721| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17041 Z= 0.141 Angle : 0.628 11.386 23026 Z= 0.326 Chirality : 0.044 0.203 2464 Planarity : 0.004 0.047 2931 Dihedral : 8.129 137.790 2373 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2012 helix: 1.02 (0.15), residues: 1158 sheet: -0.40 (0.40), residues: 169 loop : 0.10 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.041 0.002 TYR B 574 PHE 0.034 0.002 PHE C 168 TRP 0.009 0.001 TRP B 623 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17038) covalent geometry : angle 0.62429 / 0.32 (23020) SS BOND : bond 0.00663 / 0.32 ( 3) SS BOND : angle 4.20291 / 2.03 ( 6) hydrogen bonds : bond 0.03803 / 2.48 ( 912) hydrogen bonds : angle 4.97968 / 3.49 ( 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 671 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 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: symmetry clash revert: 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 8 LYS cc_start: 0.8918 (tptp) cc_final: 0.8578 (tppt) REVERT: A 113 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9203 (mmmm) REVERT: A 184 ARG cc_start: 0.9349 (mmm-85) cc_final: 0.9142 (mmm-85) REVERT: A 209 LYS cc_start: 0.9295 (tttm) cc_final: 0.9095 (tttm) REVERT: A 227 MET cc_start: 0.9287 (ptp) cc_final: 0.8996 (ptp) REVERT: A 228 LYS cc_start: 0.9073 (tptt) cc_final: 0.8589 (tptt) REVERT: A 230 LEU cc_start: 0.9742 (mt) cc_final: 0.9492 (mt) REVERT: A 250 TYR cc_start: 0.8179 (m-80) cc_final: 0.7889 (m-80) REVERT: A 254 PHE cc_start: 0.8638 (m-80) cc_final: 0.8308 (m-80) REVERT: A 262 LEU cc_start: 0.9581 (mt) cc_final: 0.9355 (mt) REVERT: A 286 ASP cc_start: 0.8819 (m-30) cc_final: 0.8611 (m-30) REVERT: A 290 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 301 PHE cc_start: 0.8822 (m-80) cc_final: 0.8363 (m-10) REVERT: A 338 ASN cc_start: 0.9326 (t0) cc_final: 0.8178 (t0) REVERT: A 348 MET cc_start: 0.8870 (ptm) cc_final: 0.8643 (ptm) REVERT: A 362 ASP cc_start: 0.8367 (m-30) cc_final: 0.8043 (m-30) REVERT: A 367 VAL cc_start: 0.9567 (m) cc_final: 0.9352 (p) REVERT: A 390 GLN cc_start: 0.8766 (mt0) cc_final: 0.8520 (mt0) REVERT: A 425 ILE cc_start: 0.8597 (mp) cc_final: 0.8333 (mp) REVERT: A 491 PHE cc_start: 0.9498 (t80) cc_final: 0.8993 (t80) REVERT: A 498 TYR cc_start: 0.8775 (m-80) cc_final: 0.8293 (m-80) REVERT: A 501 GLN cc_start: 0.9342 (tt0) cc_final: 0.8612 (tm-30) REVERT: A 505 GLU cc_start: 0.8629 (pt0) cc_final: 0.7897 (pt0) REVERT: A 515 ASP cc_start: 0.8889 (m-30) cc_final: 0.8529 (m-30) REVERT: A 558 TRP cc_start: 0.9039 (m100) cc_final: 0.8677 (m100) REVERT: A 590 SER cc_start: 0.9523 (t) cc_final: 0.9103 (p) REVERT: A 615 MET cc_start: 0.9027 (mmm) cc_final: 0.8703 (mmm) REVERT: A 645 GLN cc_start: 0.8776 (tp40) cc_final: 0.8024 (tp-100) REVERT: A 647 HIS cc_start: 0.8173 (m170) cc_final: 0.7806 (m90) REVERT: A 655 THR cc_start: 0.9122 (m) cc_final: 0.8600 (t) REVERT: A 668 ASN cc_start: 0.9284 (m-40) cc_final: 0.8872 (p0) REVERT: A 686 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7808 (mtp-110) REVERT: B 18 ILE cc_start: 0.9423 (mm) cc_final: 0.9158 (tp) REVERT: B 30 LYS cc_start: 0.9309 (tmtt) cc_final: 0.9094 (tptt) REVERT: B 87 LYS cc_start: 0.9059 (tppt) cc_final: 0.8437 (tptp) REVERT: B 95 MET cc_start: 0.8973 (tpp) cc_final: 0.8768 (tpp) REVERT: B 117 ARG cc_start: 0.8380 (mmm160) cc_final: 0.7783 (mmm-85) REVERT: B 120 ASP cc_start: 0.8705 (m-30) cc_final: 0.8330 (m-30) REVERT: B 127 LEU cc_start: 0.9776 (mt) cc_final: 0.9455 (mm) REVERT: B 129 PHE cc_start: 0.9123 (m-10) cc_final: 0.8850 (m-80) REVERT: B 147 GLN cc_start: 0.9112 (mt0) cc_final: 0.8212 (mt0) REVERT: B 150 GLN cc_start: 0.9589 (tp40) cc_final: 0.9358 (tp-100) REVERT: B 186 ILE cc_start: 0.9585 (mt) cc_final: 0.9362 (mt) REVERT: B 190 MET cc_start: 0.9196 (mtm) cc_final: 0.8977 (mtm) REVERT: B 202 ASN cc_start: 0.8288 (t0) cc_final: 0.7162 (t0) REVERT: B 231 ASP cc_start: 0.8761 (t0) cc_final: 0.7433 (t70) REVERT: B 232 ASN cc_start: 0.9148 (m-40) cc_final: 0.8634 (m110) REVERT: B 235 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.7364 (mtm-85) REVERT: B 256 ARG cc_start: 0.8285 (tmt170) cc_final: 0.7999 (ttp80) REVERT: B 258 ILE cc_start: 0.9399 (tp) cc_final: 0.9160 (tp) REVERT: B 316 GLU cc_start: 0.9199 (tt0) cc_final: 0.8994 (tt0) REVERT: B 322 MET cc_start: 0.8472 (mmt) cc_final: 0.8157 (mmm) REVERT: B 335 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 348 MET cc_start: 0.8930 (ppp) cc_final: 0.8348 (ppp) REVERT: B 349 LEU cc_start: 0.9303 (mt) cc_final: 0.8569 (mt) REVERT: B 361 GLN cc_start: 0.7851 (pp30) cc_final: 0.7357 (pp30) REVERT: B 378 PHE cc_start: 0.8929 (p90) cc_final: 0.8413 (p90) REVERT: B 425 ILE cc_start: 0.8805 (mt) cc_final: 0.8482 (mp) REVERT: B 427 LYS cc_start: 0.9047 (ptpp) cc_final: 0.8611 (pttm) REVERT: B 437 THR cc_start: 0.9513 (m) cc_final: 0.9196 (m) REVERT: B 475 ASN cc_start: 0.9062 (m-40) cc_final: 0.8796 (m110) REVERT: B 494 MET cc_start: 0.8857 (ttt) cc_final: 0.8633 (ttt) REVERT: B 546 LEU cc_start: 0.9235 (mp) cc_final: 0.9003 (mp) REVERT: B 599 GLU cc_start: 0.8951 (pm20) cc_final: 0.8749 (pm20) REVERT: B 656 LEU cc_start: 0.9251 (mt) cc_final: 0.9003 (mt) REVERT: B 658 LEU cc_start: 0.8893 (mp) cc_final: 0.8617 (mp) REVERT: B 687 THR cc_start: 0.9008 (m) cc_final: 0.7762 (m) REVERT: C 17 PHE cc_start: 0.9016 (p90) cc_final: 0.8338 (p90) REVERT: C 20 MET cc_start: 0.9402 (ppp) cc_final: 0.9164 (ppp) REVERT: C 21 PHE cc_start: 0.9064 (m-80) cc_final: 0.8514 (m-80) REVERT: C 46 TYR cc_start: 0.7795 (m-80) cc_final: 0.7418 (m-80) REVERT: C 56 MET cc_start: 0.1084 (ptm) cc_final: 0.0443 (ttp) REVERT: C 68 GLU cc_start: 0.8959 (mp0) cc_final: 0.8629 (pm20) REVERT: C 89 VAL cc_start: 0.7705 (t) cc_final: 0.6503 (p) REVERT: C 95 MET cc_start: 0.8434 (ttp) cc_final: 0.7666 (ttp) REVERT: C 174 TYR cc_start: 0.8880 (t80) cc_final: 0.7680 (t80) REVERT: C 178 PHE cc_start: 0.8964 (m-10) cc_final: 0.8318 (m-10) REVERT: C 231 LEU cc_start: 0.9174 (mt) cc_final: 0.8951 (mt) REVERT: C 315 LEU cc_start: 0.8492 (mt) cc_final: 0.7448 (mt) REVERT: D 25 ASN cc_start: 0.9256 (m-40) cc_final: 0.8801 (m-40) REVERT: D 29 PHE cc_start: 0.7341 (p90) cc_final: 0.7125 (p90) REVERT: D 185 MET cc_start: 0.6778 (ptm) cc_final: 0.6540 (ptm) REVERT: E 24 PHE cc_start: 0.9250 (m-10) cc_final: 0.8835 (m-80) REVERT: E 25 TRP cc_start: 0.8254 (p-90) cc_final: 0.7559 (p-90) REVERT: E 46 MET cc_start: 0.8322 (tpp) cc_final: 0.7977 (tpp) REVERT: E 60 ASN cc_start: 0.9342 (t0) cc_final: 0.9132 (t0) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.1306 time to fit residues: 134.6800 Evaluate side-chains 570 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 218 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 109 ASN B 320 ASN B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101259 restraints weight = 43769.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104688 restraints weight = 23442.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106842 restraints weight = 14739.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108224 restraints weight = 10654.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109187 restraints weight = 8497.696| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 17041 Z= 0.155 Angle : 0.641 11.201 23026 Z= 0.335 Chirality : 0.044 0.277 2464 Planarity : 0.004 0.046 2931 Dihedral : 7.963 138.881 2373 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2012 helix: 0.96 (0.15), residues: 1154 sheet: -0.48 (0.40), residues: 169 loop : 0.04 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 686 TYR 0.026 0.002 TYR C 174 PHE 0.037 0.002 PHE A 234 TRP 0.013 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (17038) covalent geometry : angle 0.63630 / 0.33 (23020) SS BOND : bond 0.00813 / 0.39 ( 3) SS BOND : angle 4.97830 / 2.35 ( 6) hydrogen bonds : bond 0.03849 / 2.50 ( 912) hydrogen bonds : angle 4.97304 / 3.51 ( 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 666 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 8 LYS cc_start: 0.8954 (tptp) cc_final: 0.8664 (tppt) REVERT: A 113 LYS cc_start: 0.9462 (mmtt) cc_final: 0.9182 (mmmm) REVERT: A 129 PHE cc_start: 0.9231 (m-10) cc_final: 0.8769 (m-10) REVERT: A 147 GLN cc_start: 0.8348 (tp40) cc_final: 0.8126 (tp40) REVERT: A 209 LYS cc_start: 0.9267 (tttm) cc_final: 0.9042 (tttm) REVERT: A 227 MET cc_start: 0.9318 (ptp) cc_final: 0.9037 (ptp) REVERT: A 228 LYS cc_start: 0.9050 (tptt) cc_final: 0.8580 (tptt) REVERT: A 230 LEU cc_start: 0.9715 (mt) cc_final: 0.9488 (mt) REVERT: A 250 TYR cc_start: 0.8168 (m-80) cc_final: 0.7871 (m-80) REVERT: A 252 ASN cc_start: 0.9336 (t0) cc_final: 0.9090 (t0) REVERT: A 257 ASP cc_start: 0.8743 (m-30) cc_final: 0.8447 (m-30) REVERT: A 286 ASP cc_start: 0.8870 (m-30) cc_final: 0.8643 (m-30) REVERT: A 290 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8786 (tm-30) REVERT: A 301 PHE cc_start: 0.8816 (m-80) cc_final: 0.8398 (m-10) REVERT: A 346 LEU cc_start: 0.9470 (mt) cc_final: 0.9247 (mt) REVERT: A 348 MET cc_start: 0.8891 (ptm) cc_final: 0.8643 (ptm) REVERT: A 362 ASP cc_start: 0.8442 (m-30) cc_final: 0.7979 (m-30) REVERT: A 367 VAL cc_start: 0.9596 (m) cc_final: 0.9370 (p) REVERT: A 390 GLN cc_start: 0.8820 (mt0) cc_final: 0.8538 (mt0) REVERT: A 418 ASN cc_start: 0.9056 (m-40) cc_final: 0.8712 (m110) REVERT: A 420 MET cc_start: 0.8874 (tpp) cc_final: 0.8541 (mtp) REVERT: A 489 ASN cc_start: 0.7570 (t0) cc_final: 0.7220 (t0) REVERT: A 494 MET cc_start: 0.8530 (mmp) cc_final: 0.8258 (mmp) REVERT: A 501 GLN cc_start: 0.9339 (tt0) cc_final: 0.8588 (tm-30) REVERT: A 505 GLU cc_start: 0.8641 (pt0) cc_final: 0.7972 (pt0) REVERT: A 515 ASP cc_start: 0.8904 (m-30) cc_final: 0.8553 (m-30) REVERT: A 550 MET cc_start: 0.6983 (mtm) cc_final: 0.6755 (mtt) REVERT: A 590 SER cc_start: 0.9433 (t) cc_final: 0.9132 (p) REVERT: A 615 MET cc_start: 0.8896 (mmm) cc_final: 0.8540 (mmm) REVERT: A 655 THR cc_start: 0.9138 (m) cc_final: 0.8732 (t) REVERT: A 686 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7598 (mtp-110) REVERT: B 18 ILE cc_start: 0.9410 (mm) cc_final: 0.9134 (tp) REVERT: B 30 LYS cc_start: 0.9318 (tmtt) cc_final: 0.9088 (tptt) REVERT: B 87 LYS cc_start: 0.9088 (tppt) cc_final: 0.8514 (tptp) REVERT: B 109 ASN cc_start: 0.9197 (m110) cc_final: 0.8816 (p0) REVERT: B 112 LYS cc_start: 0.9414 (mmpt) cc_final: 0.9200 (mmmt) REVERT: B 127 LEU cc_start: 0.9775 (mt) cc_final: 0.9461 (mm) REVERT: B 129 PHE cc_start: 0.9139 (m-10) cc_final: 0.8837 (m-80) REVERT: B 147 GLN cc_start: 0.9134 (mt0) cc_final: 0.8081 (mm-40) REVERT: B 150 GLN cc_start: 0.9570 (tp40) cc_final: 0.9346 (tp-100) REVERT: B 186 ILE cc_start: 0.9552 (mt) cc_final: 0.9351 (mt) REVERT: B 190 MET cc_start: 0.9276 (mtm) cc_final: 0.9056 (mtm) REVERT: B 231 ASP cc_start: 0.8689 (t0) cc_final: 0.7438 (t70) REVERT: B 232 ASN cc_start: 0.9179 (m-40) cc_final: 0.8622 (m110) REVERT: B 235 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.7326 (mtm-85) REVERT: B 256 ARG cc_start: 0.8255 (tmt170) cc_final: 0.7984 (ttp80) REVERT: B 286 ASP cc_start: 0.8391 (m-30) cc_final: 0.8120 (m-30) REVERT: B 322 MET cc_start: 0.8485 (mmt) cc_final: 0.8202 (mmm) REVERT: B 348 MET cc_start: 0.9019 (ppp) cc_final: 0.8482 (ppp) REVERT: B 349 LEU cc_start: 0.9322 (mt) cc_final: 0.8615 (mt) REVERT: B 361 GLN cc_start: 0.7836 (pp30) cc_final: 0.7330 (pp30) REVERT: B 378 PHE cc_start: 0.8952 (p90) cc_final: 0.8456 (p90) REVERT: B 427 LYS cc_start: 0.9061 (ptpp) cc_final: 0.8771 (pttm) REVERT: B 434 ASP cc_start: 0.9059 (m-30) cc_final: 0.8835 (m-30) REVERT: B 437 THR cc_start: 0.9504 (m) cc_final: 0.9148 (m) REVERT: B 475 ASN cc_start: 0.9239 (m-40) cc_final: 0.8979 (m110) REVERT: B 575 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8125 (ptp90) REVERT: B 612 TYR cc_start: 0.8425 (m-80) cc_final: 0.8162 (m-80) REVERT: B 632 MET cc_start: 0.7704 (ptp) cc_final: 0.7308 (ptp) REVERT: B 656 LEU cc_start: 0.9230 (mt) cc_final: 0.8969 (mt) REVERT: B 670 ILE cc_start: 0.9301 (mt) cc_final: 0.9074 (mt) REVERT: B 686 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8173 (tpt170) REVERT: C 17 PHE cc_start: 0.9054 (p90) cc_final: 0.8344 (p90) REVERT: C 20 MET cc_start: 0.9445 (ppp) cc_final: 0.9222 (ppp) REVERT: C 21 PHE cc_start: 0.9087 (m-80) cc_final: 0.8552 (m-80) REVERT: C 46 TYR cc_start: 0.7811 (m-80) cc_final: 0.7437 (m-80) REVERT: C 56 MET cc_start: 0.0969 (ptm) cc_final: 0.0063 (ttm) REVERT: C 74 MET cc_start: 0.9311 (mpp) cc_final: 0.8985 (mpp) REVERT: C 89 VAL cc_start: 0.7725 (t) cc_final: 0.7220 (t) REVERT: C 95 MET cc_start: 0.8496 (ttp) cc_final: 0.7691 (ttp) REVERT: C 174 TYR cc_start: 0.8852 (t80) cc_final: 0.7579 (t80) REVERT: C 178 PHE cc_start: 0.9012 (m-10) cc_final: 0.8302 (m-10) REVERT: C 231 LEU cc_start: 0.9191 (mt) cc_final: 0.8978 (mt) REVERT: D 25 ASN cc_start: 0.9325 (m-40) cc_final: 0.8851 (m-40) REVERT: D 29 PHE cc_start: 0.7400 (p90) cc_final: 0.7172 (p90) REVERT: D 92 PHE cc_start: 0.6859 (t80) cc_final: 0.6361 (t80) REVERT: D 185 MET cc_start: 0.6503 (ptm) cc_final: 0.6291 (ptm) REVERT: D 238 ASN cc_start: 0.8501 (m110) cc_final: 0.8284 (m110) REVERT: E 24 PHE cc_start: 0.9287 (m-10) cc_final: 0.9048 (m-80) REVERT: E 25 TRP cc_start: 0.8149 (p-90) cc_final: 0.7903 (p-90) REVERT: E 46 MET cc_start: 0.8186 (tpp) cc_final: 0.7872 (tpp) REVERT: E 60 ASN cc_start: 0.9370 (t0) cc_final: 0.9134 (t0) REVERT: E 67 TYR cc_start: 0.8788 (m-10) cc_final: 0.8532 (m-10) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.1309 time to fit residues: 134.0385 Evaluate side-chains 557 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101100 restraints weight = 43146.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104615 restraints weight = 22796.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106924 restraints weight = 14445.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108506 restraints weight = 10288.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109465 restraints weight = 8040.329| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 17041 Z= 0.155 Angle : 0.668 11.447 23026 Z= 0.350 Chirality : 0.045 0.234 2464 Planarity : 0.004 0.052 2931 Dihedral : 7.901 139.687 2373 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2012 helix: 0.92 (0.15), residues: 1150 sheet: -0.25 (0.41), residues: 157 loop : -0.04 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 350 TYR 0.025 0.002 TYR C 130 PHE 0.035 0.002 PHE A 378 TRP 0.013 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17038) covalent geometry : angle 0.66522 / 0.35 (23020) SS BOND : bond 0.00860 / 0.41 ( 3) SS BOND : angle 4.08329 / 1.97 ( 6) hydrogen bonds : bond 0.03902 / 2.52 ( 912) hydrogen bonds : angle 5.04221 / 3.57 ( 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 658 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8940 (tptp) cc_final: 0.8645 (tppt) REVERT: A 113 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9190 (mmmm) REVERT: A 129 PHE cc_start: 0.9176 (m-10) cc_final: 0.8869 (m-10) REVERT: A 147 GLN cc_start: 0.8410 (tp40) cc_final: 0.8043 (tp-100) REVERT: A 157 LEU cc_start: 0.9175 (tp) cc_final: 0.8884 (tp) REVERT: A 187 ASP cc_start: 0.8734 (t70) cc_final: 0.8531 (t0) REVERT: A 227 MET cc_start: 0.9292 (ptp) cc_final: 0.9069 (ptp) REVERT: A 228 LYS cc_start: 0.9077 (tptt) cc_final: 0.8615 (tptt) REVERT: A 250 TYR cc_start: 0.8200 (m-80) cc_final: 0.7897 (m-80) REVERT: A 252 ASN cc_start: 0.9293 (t0) cc_final: 0.8976 (t0) REVERT: A 254 PHE cc_start: 0.8661 (m-80) cc_final: 0.8404 (m-80) REVERT: A 290 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 301 PHE cc_start: 0.8801 (m-80) cc_final: 0.8428 (m-10) REVERT: A 314 MET cc_start: 0.8446 (ttm) cc_final: 0.8225 (ttt) REVERT: A 346 LEU cc_start: 0.9469 (mt) cc_final: 0.9223 (mt) REVERT: A 362 ASP cc_start: 0.8376 (m-30) cc_final: 0.7902 (m-30) REVERT: A 367 VAL cc_start: 0.9556 (m) cc_final: 0.9320 (p) REVERT: A 390 GLN cc_start: 0.8821 (mt0) cc_final: 0.8544 (mt0) REVERT: A 417 LEU cc_start: 0.9182 (tp) cc_final: 0.8855 (tp) REVERT: A 494 MET cc_start: 0.8565 (mmp) cc_final: 0.8346 (mmp) REVERT: A 501 GLN cc_start: 0.9337 (tt0) cc_final: 0.8610 (tm-30) REVERT: A 505 GLU cc_start: 0.8654 (pt0) cc_final: 0.8004 (pt0) REVERT: A 515 ASP cc_start: 0.8889 (m-30) cc_final: 0.8547 (m-30) REVERT: A 615 MET cc_start: 0.8873 (mmm) cc_final: 0.8539 (mmm) REVERT: A 645 GLN cc_start: 0.8806 (tp40) cc_final: 0.8001 (tp40) REVERT: A 655 THR cc_start: 0.9185 (m) cc_final: 0.8656 (t) REVERT: A 686 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7895 (mtp180) REVERT: B 30 LYS cc_start: 0.9312 (tmtt) cc_final: 0.9088 (tptt) REVERT: B 87 LYS cc_start: 0.9058 (tppt) cc_final: 0.8515 (tptp) REVERT: B 109 ASN cc_start: 0.9155 (m110) cc_final: 0.8776 (p0) REVERT: B 127 LEU cc_start: 0.9764 (mt) cc_final: 0.9452 (mm) REVERT: B 129 PHE cc_start: 0.9117 (m-10) cc_final: 0.8829 (m-80) REVERT: B 147 GLN cc_start: 0.9104 (mt0) cc_final: 0.8073 (mm-40) REVERT: B 186 ILE cc_start: 0.9570 (mt) cc_final: 0.9331 (mt) REVERT: B 190 MET cc_start: 0.9243 (mtm) cc_final: 0.9037 (mtm) REVERT: B 223 VAL cc_start: 0.9611 (m) cc_final: 0.9369 (p) REVERT: B 232 ASN cc_start: 0.9082 (m-40) cc_final: 0.8750 (m110) REVERT: B 240 MET cc_start: 0.7781 (ppp) cc_final: 0.7201 (ppp) REVERT: B 256 ARG cc_start: 0.8221 (tmt170) cc_final: 0.7964 (ttp80) REVERT: B 286 ASP cc_start: 0.8404 (m-30) cc_final: 0.8154 (m-30) REVERT: B 322 MET cc_start: 0.8511 (mmt) cc_final: 0.7810 (mmm) REVERT: B 335 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 348 MET cc_start: 0.9008 (ppp) cc_final: 0.8461 (ppp) REVERT: B 349 LEU cc_start: 0.9312 (mt) cc_final: 0.8607 (mt) REVERT: B 361 GLN cc_start: 0.7807 (pp30) cc_final: 0.7326 (pp30) REVERT: B 378 PHE cc_start: 0.8964 (p90) cc_final: 0.8376 (p90) REVERT: B 425 ILE cc_start: 0.8838 (mt) cc_final: 0.8051 (mt) REVERT: B 437 THR cc_start: 0.9483 (m) cc_final: 0.9140 (m) REVERT: B 466 MET cc_start: 0.8416 (ptt) cc_final: 0.8179 (ptt) REVERT: B 475 ASN cc_start: 0.9247 (m-40) cc_final: 0.8960 (m110) REVERT: B 494 MET cc_start: 0.8925 (ttt) cc_final: 0.8654 (ttt) REVERT: B 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8586 (m-30) REVERT: B 546 LEU cc_start: 0.9392 (mt) cc_final: 0.9185 (mp) REVERT: B 575 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8125 (ptp90) REVERT: B 604 ARG cc_start: 0.9253 (mmm160) cc_final: 0.9037 (mmm160) REVERT: B 612 TYR cc_start: 0.8372 (m-80) cc_final: 0.7767 (m-80) REVERT: B 624 PHE cc_start: 0.8500 (m-80) cc_final: 0.8292 (m-80) REVERT: B 670 ILE cc_start: 0.9301 (mt) cc_final: 0.9099 (mt) REVERT: B 686 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8073 (tpt170) REVERT: C 17 PHE cc_start: 0.9066 (p90) cc_final: 0.8359 (p90) REVERT: C 20 MET cc_start: 0.9429 (ppp) cc_final: 0.9185 (ppp) REVERT: C 21 PHE cc_start: 0.9084 (m-80) cc_final: 0.8542 (m-80) REVERT: C 46 TYR cc_start: 0.7787 (m-80) cc_final: 0.7434 (m-80) REVERT: C 56 MET cc_start: 0.1073 (ptm) cc_final: 0.0472 (ttp) REVERT: C 68 GLU cc_start: 0.8989 (mp0) cc_final: 0.8547 (pm20) REVERT: C 74 MET cc_start: 0.9303 (mpp) cc_final: 0.8969 (mpp) REVERT: C 89 VAL cc_start: 0.7807 (t) cc_final: 0.7227 (t) REVERT: C 95 MET cc_start: 0.8495 (ttp) cc_final: 0.7570 (ttp) REVERT: C 157 MET cc_start: 0.9296 (mtm) cc_final: 0.8897 (ptp) REVERT: C 174 TYR cc_start: 0.8814 (t80) cc_final: 0.7517 (t80) REVERT: C 178 PHE cc_start: 0.8994 (m-10) cc_final: 0.8225 (m-10) REVERT: C 226 GLU cc_start: 0.8851 (pt0) cc_final: 0.8519 (pt0) REVERT: C 231 LEU cc_start: 0.9283 (mt) cc_final: 0.9066 (mt) REVERT: C 274 ASP cc_start: 0.8921 (p0) cc_final: 0.8664 (p0) REVERT: D 25 ASN cc_start: 0.9366 (m-40) cc_final: 0.8913 (m-40) REVERT: D 29 PHE cc_start: 0.7458 (p90) cc_final: 0.7222 (p90) REVERT: D 92 PHE cc_start: 0.6958 (t80) cc_final: 0.6104 (t80) REVERT: E 24 PHE cc_start: 0.9303 (m-10) cc_final: 0.9060 (m-80) REVERT: E 25 TRP cc_start: 0.8316 (p-90) cc_final: 0.8072 (p-90) REVERT: E 46 MET cc_start: 0.8230 (tpp) cc_final: 0.7908 (tpp) REVERT: E 60 ASN cc_start: 0.9316 (t0) cc_final: 0.9072 (t0) REVERT: E 67 TYR cc_start: 0.8811 (m-10) cc_final: 0.8534 (m-10) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.1327 time to fit residues: 134.1727 Evaluate side-chains 567 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 158 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096383 restraints weight = 43242.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099595 restraints weight = 23368.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101732 restraints weight = 14937.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103085 restraints weight = 10728.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104069 restraints weight = 8519.381| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (18 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17041 Z= 0.188 Angle : 0.698 12.835 23026 Z= 0.364 Chirality : 0.045 0.208 2464 Planarity : 0.004 0.051 2931 Dihedral : 7.980 141.568 2373 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2012 helix: 0.83 (0.15), residues: 1140 sheet: -0.31 (0.41), residues: 165 loop : -0.21 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 184 TYR 0.030 0.002 TYR C 173 PHE 0.037 0.002 PHE C 172 TRP 0.021 0.002 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (17038) covalent geometry : angle 0.69484 / 0.36 (23020) SS BOND : bond 0.00736 / 0.35 ( 3) SS BOND : angle 4.04965 / 1.98 ( 6) hydrogen bonds : bond 0.03981 / 2.59 ( 912) hydrogen bonds : angle 5.09778 / 3.60 ( 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 628 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8929 (tptp) cc_final: 0.8649 (tppt) REVERT: A 113 LYS cc_start: 0.9470 (mmtt) cc_final: 0.9219 (mmmm) REVERT: A 181 ASP cc_start: 0.8980 (m-30) cc_final: 0.8724 (m-30) REVERT: A 184 ARG cc_start: 0.9325 (mmm-85) cc_final: 0.8922 (mmm160) REVERT: A 187 ASP cc_start: 0.8812 (t70) cc_final: 0.8501 (t0) REVERT: A 227 MET cc_start: 0.9398 (ptp) cc_final: 0.8994 (ptp) REVERT: A 228 LYS cc_start: 0.9105 (tptt) cc_final: 0.8603 (tptt) REVERT: A 250 TYR cc_start: 0.8296 (m-80) cc_final: 0.7923 (m-80) REVERT: A 254 PHE cc_start: 0.8738 (m-80) cc_final: 0.8383 (m-80) REVERT: A 290 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 291 LEU cc_start: 0.9478 (mm) cc_final: 0.8979 (mm) REVERT: A 301 PHE cc_start: 0.8815 (m-80) cc_final: 0.8398 (m-10) REVERT: A 367 VAL cc_start: 0.9528 (m) cc_final: 0.9316 (p) REVERT: A 390 GLN cc_start: 0.8863 (mt0) cc_final: 0.8618 (mt0) REVERT: A 456 LYS cc_start: 0.9335 (ptmt) cc_final: 0.8992 (pttp) REVERT: A 491 PHE cc_start: 0.9337 (t80) cc_final: 0.8948 (t80) REVERT: A 501 GLN cc_start: 0.9341 (tt0) cc_final: 0.8612 (tm-30) REVERT: A 505 GLU cc_start: 0.8658 (pt0) cc_final: 0.8046 (pt0) REVERT: A 515 ASP cc_start: 0.8908 (m-30) cc_final: 0.8596 (m-30) REVERT: A 615 MET cc_start: 0.8911 (mmm) cc_final: 0.8594 (mmm) REVERT: A 645 GLN cc_start: 0.9081 (tp40) cc_final: 0.8820 (tp-100) REVERT: A 655 THR cc_start: 0.9078 (m) cc_final: 0.8831 (t) REVERT: B 18 ILE cc_start: 0.9436 (mm) cc_final: 0.9088 (mm) REVERT: B 30 LYS cc_start: 0.9324 (tmtt) cc_final: 0.9091 (tptt) REVERT: B 87 LYS cc_start: 0.9098 (tppt) cc_final: 0.8581 (tptp) REVERT: B 109 ASN cc_start: 0.9187 (m110) cc_final: 0.8774 (p0) REVERT: B 120 ASP cc_start: 0.8854 (m-30) cc_final: 0.8647 (m-30) REVERT: B 127 LEU cc_start: 0.9768 (mt) cc_final: 0.9465 (mm) REVERT: B 129 PHE cc_start: 0.9096 (m-10) cc_final: 0.8833 (m-80) REVERT: B 147 GLN cc_start: 0.9132 (mt0) cc_final: 0.8160 (mt0) REVERT: B 150 GLN cc_start: 0.9190 (tp40) cc_final: 0.8914 (tp-100) REVERT: B 190 MET cc_start: 0.9325 (mtm) cc_final: 0.9063 (mtm) REVERT: B 223 VAL cc_start: 0.9621 (m) cc_final: 0.9374 (p) REVERT: B 231 ASP cc_start: 0.8689 (t70) cc_final: 0.7486 (t70) REVERT: B 232 ASN cc_start: 0.9053 (m-40) cc_final: 0.8714 (m110) REVERT: B 235 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8086 (mtm-85) REVERT: B 240 MET cc_start: 0.7822 (ppp) cc_final: 0.7207 (ppp) REVERT: B 256 ARG cc_start: 0.8201 (tmt170) cc_final: 0.7984 (ttp80) REVERT: B 316 GLU cc_start: 0.8984 (tt0) cc_final: 0.8546 (tt0) REVERT: B 322 MET cc_start: 0.8460 (mmt) cc_final: 0.8201 (mmm) REVERT: B 335 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 348 MET cc_start: 0.8997 (ppp) cc_final: 0.8432 (ppp) REVERT: B 349 LEU cc_start: 0.9333 (mt) cc_final: 0.8610 (mt) REVERT: B 361 GLN cc_start: 0.8011 (pp30) cc_final: 0.7506 (pp30) REVERT: B 378 PHE cc_start: 0.8868 (p90) cc_final: 0.8399 (p90) REVERT: B 384 GLU cc_start: 0.8165 (pp20) cc_final: 0.7679 (pp20) REVERT: B 427 LYS cc_start: 0.9100 (ptpp) cc_final: 0.8731 (pttm) REVERT: B 434 ASP cc_start: 0.9052 (m-30) cc_final: 0.8829 (m-30) REVERT: B 437 THR cc_start: 0.9483 (m) cc_final: 0.9102 (m) REVERT: B 475 ASN cc_start: 0.9241 (m-40) cc_final: 0.8924 (m110) REVERT: B 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8585 (p0) REVERT: B 575 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8171 (ptp90) REVERT: B 604 ARG cc_start: 0.9271 (mmm160) cc_final: 0.8958 (mmm160) REVERT: B 612 TYR cc_start: 0.8427 (m-80) cc_final: 0.8220 (m-80) REVERT: B 637 VAL cc_start: 0.9070 (t) cc_final: 0.8867 (t) REVERT: B 656 LEU cc_start: 0.9264 (mt) cc_final: 0.8985 (mt) REVERT: C 17 PHE cc_start: 0.9139 (p90) cc_final: 0.8418 (p90) REVERT: C 20 MET cc_start: 0.9423 (ppp) cc_final: 0.9183 (ppp) REVERT: C 21 PHE cc_start: 0.9130 (m-80) cc_final: 0.8591 (m-80) REVERT: C 46 TYR cc_start: 0.7777 (m-80) cc_final: 0.7494 (m-80) REVERT: C 56 MET cc_start: 0.0798 (ptm) cc_final: 0.0182 (ttp) REVERT: C 68 GLU cc_start: 0.8967 (mp0) cc_final: 0.8505 (pm20) REVERT: C 74 MET cc_start: 0.9291 (mpp) cc_final: 0.8911 (mpp) REVERT: C 89 VAL cc_start: 0.7712 (t) cc_final: 0.7154 (t) REVERT: C 95 MET cc_start: 0.8581 (ttp) cc_final: 0.7741 (ttp) REVERT: C 157 MET cc_start: 0.9343 (mtm) cc_final: 0.8802 (ptp) REVERT: C 174 TYR cc_start: 0.8799 (t80) cc_final: 0.7529 (t80) REVERT: C 178 PHE cc_start: 0.9002 (m-10) cc_final: 0.8275 (m-10) REVERT: C 226 GLU cc_start: 0.8934 (pt0) cc_final: 0.8609 (pt0) REVERT: C 231 LEU cc_start: 0.9275 (mt) cc_final: 0.9052 (mt) REVERT: C 274 ASP cc_start: 0.8882 (p0) cc_final: 0.8570 (p0) REVERT: D 25 ASN cc_start: 0.9360 (m-40) cc_final: 0.8941 (m-40) REVERT: D 92 PHE cc_start: 0.6990 (t80) cc_final: 0.6178 (t80) REVERT: D 212 ILE cc_start: 0.8639 (mm) cc_final: 0.8315 (tt) REVERT: E 24 PHE cc_start: 0.9295 (m-10) cc_final: 0.8940 (m-80) REVERT: E 25 TRP cc_start: 0.8227 (p-90) cc_final: 0.7932 (p-90) REVERT: E 46 MET cc_start: 0.8194 (tpp) cc_final: 0.7916 (tpp) REVERT: E 60 ASN cc_start: 0.9338 (t0) cc_final: 0.9089 (t0) REVERT: E 67 TYR cc_start: 0.8805 (m-10) cc_final: 0.8562 (m-10) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.1228 time to fit residues: 118.6256 Evaluate side-chains 549 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 127 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS D 28 GLN D 132 GLN D 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100053 restraints weight = 42676.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103690 restraints weight = 22947.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106069 restraints weight = 14482.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107523 restraints weight = 10351.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108692 restraints weight = 8197.654| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17041 Z= 0.136 Angle : 0.674 13.053 23026 Z= 0.351 Chirality : 0.045 0.175 2464 Planarity : 0.004 0.051 2931 Dihedral : 7.782 139.574 2373 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2012 helix: 0.84 (0.15), residues: 1135 sheet: 0.15 (0.44), residues: 145 loop : -0.23 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 184 TYR 0.025 0.001 TYR C 174 PHE 0.035 0.002 PHE C 172 TRP 0.011 0.001 TRP D 124 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (17038) covalent geometry : angle 0.67086 / 0.35 (23020) SS BOND : bond 0.00698 / 0.34 ( 3) SS BOND : angle 3.77690 / 1.83 ( 6) hydrogen bonds : bond 0.03816 / 2.45 ( 912) hydrogen bonds : angle 5.01033 / 3.53 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.78 seconds wall clock time: 69 minutes 13.60 seconds (4153.60 seconds total)