Starting phenix.real_space_refine on Fri Jul 3 22:04:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9by0_45016/07_2026/9by0_45016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9by0_45016/07_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_45016/07_2026/9by0_45016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9by0_45016/07_2026/9by0_45016.map" model { file = "/net/cci-nas-00/data/ceres_data/9by0_45016/07_2026/9by0_45016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9by0_45016/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.24, per 1000 atoms: 0.19 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: 1.19 Conformation dependent library (CDL) restraints added in 758.3 milliseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 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: 2.70 Time building geometry restraints manager: 1.56 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 3.060 ... (remaining 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: 1.250 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- 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 : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1444 time to fit residues: 202.5251 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 : 0.593 ------------------------------------------------------------------------------- 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 61 ASN B 191 GLN B 304 HIS B 320 ASN B 370 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094216 restraints weight = 41642.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098058 restraints weight = 21385.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100577 restraints weight = 13238.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102132 restraints weight = 9311.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103308 restraints weight = 7274.206| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4374 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= 0.199 Angle : 0.690 14.052 23026 Z= 0.364 Chirality : 0.044 0.242 2464 Planarity : 0.004 0.048 2931 Dihedral : 9.057 136.156 2373 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.28 % Allowed : 2.91 % 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: 1.25 (0.18), residues: 2012 helix: 1.26 (0.15), residues: 1160 sheet: -0.31 (0.38), residues: 163 loop : 0.60 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.030 0.002 TYR C 174 PHE 0.031 0.002 PHE C 168 TRP 0.021 0.002 TRP B 623 HIS 0.009 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (17038) covalent geometry : angle 0.67739 / 0.36 (23020) SS BOND : bond 0.00429 / 0.20 ( 3) SS BOND : angle 8.01290 / 4.16 ( 6) hydrogen bonds : bond 0.04907 / 3.20 ( 912) hydrogen bonds : angle 5.13347 / 3.55 ( 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 747 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 742 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.9071 (tp) cc_final: 0.8781 (tp) REVERT: A 147 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7889 (tp40) REVERT: A 223 VAL cc_start: 0.9462 (m) cc_final: 0.9159 (p) REVERT: A 227 MET cc_start: 0.9336 (mtm) cc_final: 0.9106 (mtm) REVERT: A 338 ASN cc_start: 0.9549 (t0) cc_final: 0.7920 (t0) REVERT: A 341 LYS cc_start: 0.9685 (mmtp) cc_final: 0.9377 (mmtp) REVERT: A 346 LEU cc_start: 0.9511 (mt) cc_final: 0.9301 (mt) REVERT: A 367 VAL cc_start: 0.9558 (m) cc_final: 0.9284 (p) REVERT: A 421 GLU cc_start: 0.8229 (pp20) cc_final: 0.7857 (pp20) REVERT: A 453 ARG cc_start: 0.9180 (ttt-90) cc_final: 0.8845 (ttt-90) REVERT: A 475 ASN cc_start: 0.8296 (m110) cc_final: 0.7866 (m110) REVERT: A 509 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 518 GLU cc_start: 0.8894 (pp20) cc_final: 0.8569 (pp20) REVERT: A 528 PHE cc_start: 0.8281 (m-10) cc_final: 0.7895 (m-80) REVERT: A 558 TRP cc_start: 0.8866 (m100) cc_final: 0.8479 (m100) REVERT: A 639 ASP cc_start: 0.8897 (m-30) cc_final: 0.8596 (m-30) REVERT: A 658 LEU cc_start: 0.9576 (mp) cc_final: 0.9321 (mp) REVERT: B 18 ILE cc_start: 0.9371 (mm) cc_final: 0.8799 (mm) REVERT: B 41 ILE cc_start: 0.9453 (mm) cc_final: 0.9210 (mt) REVERT: B 127 LEU cc_start: 0.9780 (mt) cc_final: 0.9479 (mm) REVERT: B 135 GLU cc_start: 0.9153 (mp0) cc_final: 0.8821 (pm20) REVERT: B 147 GLN cc_start: 0.9023 (mt0) cc_final: 0.8579 (mt0) REVERT: B 156 PHE cc_start: 0.9265 (t80) cc_final: 0.9034 (t80) REVERT: B 186 ILE cc_start: 0.9649 (mt) cc_final: 0.9091 (mt) REVERT: B 190 MET cc_start: 0.9344 (mtm) cc_final: 0.8909 (mtm) REVERT: B 227 MET cc_start: 0.9171 (mtp) cc_final: 0.8923 (mtp) REVERT: B 286 ASP cc_start: 0.8391 (m-30) cc_final: 0.8121 (m-30) REVERT: B 348 MET cc_start: 0.9043 (ppp) cc_final: 0.8478 (ppp) REVERT: B 349 LEU cc_start: 0.9377 (mt) cc_final: 0.8936 (mt) REVERT: B 370 ASN cc_start: 0.9277 (m-40) cc_final: 0.8616 (m110) REVERT: B 402 GLU cc_start: 0.7970 (mp0) cc_final: 0.7541 (mp0) REVERT: B 420 MET cc_start: 0.9282 (mmp) cc_final: 0.9063 (mmp) REVERT: B 475 ASN cc_start: 0.9027 (m110) cc_final: 0.8718 (m110) REVERT: B 515 ASP cc_start: 0.8911 (m-30) cc_final: 0.8457 (p0) REVERT: B 546 LEU cc_start: 0.9448 (mm) cc_final: 0.9122 (mp) REVERT: B 558 TRP cc_start: 0.8729 (m100) cc_final: 0.8329 (m100) REVERT: B 574 TYR cc_start: 0.8280 (m-80) cc_final: 0.7906 (m-80) REVERT: B 586 TYR cc_start: 0.8971 (m-80) cc_final: 0.8621 (m-80) REVERT: B 623 TRP cc_start: 0.8384 (t-100) cc_final: 0.8132 (t-100) REVERT: B 634 MET cc_start: 0.8047 (mmp) cc_final: 0.7733 (mmt) REVERT: B 656 LEU cc_start: 0.9311 (mt) cc_final: 0.9039 (mt) REVERT: C 21 PHE cc_start: 0.9008 (m-80) cc_final: 0.8528 (m-80) REVERT: C 23 ASN cc_start: 0.9715 (m-40) cc_final: 0.9468 (m-40) REVERT: C 74 MET cc_start: 0.9370 (mpp) cc_final: 0.9050 (mpp) REVERT: C 101 HIS cc_start: 0.4831 (m170) cc_final: 0.4334 (m-70) REVERT: C 157 MET cc_start: 0.9357 (mtm) cc_final: 0.8927 (ptt) REVERT: C 163 LEU cc_start: 0.9141 (tt) cc_final: 0.8860 (tp) REVERT: C 174 TYR cc_start: 0.8852 (t80) cc_final: 0.7648 (t80) REVERT: C 212 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 231 LEU cc_start: 0.8822 (tp) cc_final: 0.8492 (tp) REVERT: C 233 ASN cc_start: 0.9320 (m-40) cc_final: 0.9119 (m-40) REVERT: C 285 ILE cc_start: 0.6663 (tp) cc_final: 0.6241 (tp) REVERT: D 16 ASP cc_start: 0.6791 (t0) cc_final: 0.6513 (t0) REVERT: D 109 PHE cc_start: 0.8706 (m-10) cc_final: 0.8500 (m-80) REVERT: D 115 THR cc_start: 0.8482 (m) cc_final: 0.8250 (p) REVERT: D 119 ASN cc_start: 0.8505 (m110) cc_final: 0.8154 (m-40) REVERT: D 128 ASN cc_start: 0.8957 (t0) cc_final: 0.8106 (t0) REVERT: D 133 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7742 (tptp) REVERT: E 25 TRP cc_start: 0.8164 (p-90) cc_final: 0.7757 (p-90) REVERT: E 46 MET cc_start: 0.8154 (tpp) cc_final: 0.7048 (mpp) REVERT: E 70 MET cc_start: 0.8181 (mmp) cc_final: 0.7143 (mpp) outliers start: 5 outliers final: 1 residues processed: 743 average time/residue: 0.1368 time to fit residues: 154.5335 Evaluate side-chains 599 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 597 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 10.0000 chunk 138 optimal weight: 10.0000 chunk 156 optimal weight: 0.3980 chunk 130 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 120 optimal weight: 0.0170 chunk 128 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- 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 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 D 201 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094774 restraints weight = 43126.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098201 restraints weight = 23350.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100426 restraints weight = 14882.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101989 restraints weight = 10613.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103019 restraints weight = 8277.347| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17041 Z= 0.179 Angle : 0.628 13.249 23026 Z= 0.330 Chirality : 0.044 0.281 2464 Planarity : 0.004 0.053 2931 Dihedral : 8.771 136.958 2373 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2012 helix: 1.29 (0.15), residues: 1151 sheet: -0.19 (0.39), residues: 167 loop : 0.39 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 225 TYR 0.028 0.002 TYR C 174 PHE 0.033 0.002 PHE C 166 TRP 0.012 0.001 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (17038) covalent geometry : angle 0.62547 / 0.33 (23020) SS BOND : bond 0.00779 / 0.37 ( 3) SS BOND : angle 3.19582 / 1.64 ( 6) hydrogen bonds : bond 0.04364 / 2.84 ( 912) hydrogen bonds : angle 4.93513 / 3.41 ( 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 726 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 726 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9136 (mp0) cc_final: 0.8915 (mm-30) REVERT: A 119 GLU cc_start: 0.8504 (mp0) cc_final: 0.8272 (mm-30) REVERT: A 223 VAL cc_start: 0.9492 (m) cc_final: 0.9166 (p) REVERT: A 254 PHE cc_start: 0.8809 (m-80) cc_final: 0.8424 (m-80) REVERT: A 286 ASP cc_start: 0.8706 (m-30) cc_final: 0.8456 (m-30) REVERT: A 346 LEU cc_start: 0.9504 (mt) cc_final: 0.9298 (mt) REVERT: A 367 VAL cc_start: 0.9588 (m) cc_final: 0.9335 (p) REVERT: A 390 GLN cc_start: 0.8661 (mt0) cc_final: 0.8362 (mt0) REVERT: A 403 ILE cc_start: 0.9204 (mp) cc_final: 0.8808 (mp) REVERT: A 417 LEU cc_start: 0.9395 (tp) cc_final: 0.9152 (tp) REVERT: A 421 GLU cc_start: 0.8339 (pp20) cc_final: 0.8074 (pp20) REVERT: A 453 ARG cc_start: 0.9217 (ttt-90) cc_final: 0.8885 (ttt-90) REVERT: A 475 ASN cc_start: 0.8430 (m110) cc_final: 0.7765 (m-40) REVERT: A 501 GLN cc_start: 0.8950 (tt0) cc_final: 0.8604 (tt0) REVERT: A 509 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 558 TRP cc_start: 0.8990 (m100) cc_final: 0.8659 (m100) REVERT: A 615 MET cc_start: 0.8917 (mmm) cc_final: 0.8587 (mmm) REVERT: A 658 LEU cc_start: 0.9578 (mp) cc_final: 0.9346 (mp) REVERT: A 686 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7280 (mtp85) REVERT: B 30 LYS cc_start: 0.9121 (tptt) cc_final: 0.8799 (tptp) REVERT: B 127 LEU cc_start: 0.9789 (mt) cc_final: 0.9520 (mm) REVERT: B 129 PHE cc_start: 0.9207 (m-80) cc_final: 0.8925 (m-80) REVERT: B 135 GLU cc_start: 0.9059 (mp0) cc_final: 0.8827 (pm20) REVERT: B 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8638 (mt0) REVERT: B 150 GLN cc_start: 0.9362 (tp40) cc_final: 0.8793 (tp-100) REVERT: B 156 PHE cc_start: 0.9291 (t80) cc_final: 0.9079 (t80) REVERT: B 184 ARG cc_start: 0.9521 (tpp80) cc_final: 0.9197 (tpp80) REVERT: B 232 ASN cc_start: 0.9170 (m-40) cc_final: 0.8728 (m110) REVERT: B 252 ASN cc_start: 0.9396 (t0) cc_final: 0.9003 (t0) REVERT: B 286 ASP cc_start: 0.8335 (m-30) cc_final: 0.8064 (m-30) REVERT: B 322 MET cc_start: 0.8439 (mmt) cc_final: 0.8216 (mmm) REVERT: B 335 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 348 MET cc_start: 0.8954 (ppp) cc_final: 0.8465 (ppp) REVERT: B 349 LEU cc_start: 0.9370 (mt) cc_final: 0.8845 (mt) REVERT: B 370 ASN cc_start: 0.9543 (m-40) cc_final: 0.9089 (m110) REVERT: B 378 PHE cc_start: 0.8879 (p90) cc_final: 0.8593 (p90) REVERT: B 402 GLU cc_start: 0.8128 (mp0) cc_final: 0.7753 (mp0) REVERT: B 475 ASN cc_start: 0.9002 (m-40) cc_final: 0.8682 (m110) REVERT: B 490 THR cc_start: 0.9267 (m) cc_final: 0.9025 (p) REVERT: B 515 ASP cc_start: 0.8954 (m-30) cc_final: 0.8547 (p0) REVERT: B 574 TYR cc_start: 0.8455 (m-80) cc_final: 0.8241 (m-80) REVERT: B 586 TYR cc_start: 0.9004 (m-80) cc_final: 0.8714 (m-80) REVERT: B 598 MET cc_start: 0.8149 (mtp) cc_final: 0.7848 (mtt) REVERT: B 599 GLU cc_start: 0.8656 (mp0) cc_final: 0.8361 (mp0) REVERT: B 612 TYR cc_start: 0.8392 (m-80) cc_final: 0.7884 (m-80) REVERT: B 623 TRP cc_start: 0.8458 (t-100) cc_final: 0.8006 (t-100) REVERT: B 650 GLN cc_start: 0.6931 (mt0) cc_final: 0.6546 (mt0) REVERT: B 656 LEU cc_start: 0.9334 (mt) cc_final: 0.9045 (mt) REVERT: C 17 PHE cc_start: 0.8942 (p90) cc_final: 0.8244 (p90) REVERT: C 20 MET cc_start: 0.9106 (ppp) cc_final: 0.8868 (ppp) REVERT: C 21 PHE cc_start: 0.8981 (m-80) cc_final: 0.8284 (m-80) REVERT: C 74 MET cc_start: 0.9399 (mpp) cc_final: 0.9005 (mpp) REVERT: C 93 MET cc_start: 0.9254 (mtt) cc_final: 0.9029 (mtt) REVERT: C 95 MET cc_start: 0.8586 (ttp) cc_final: 0.7982 (ttp) REVERT: C 157 MET cc_start: 0.9426 (mtm) cc_final: 0.9019 (ptp) REVERT: C 163 LEU cc_start: 0.9175 (tt) cc_final: 0.8703 (tt) REVERT: C 174 TYR cc_start: 0.8777 (t80) cc_final: 0.7296 (t80) REVERT: C 178 PHE cc_start: 0.8866 (m-10) cc_final: 0.8026 (m-10) REVERT: C 212 ILE cc_start: 0.8670 (mt) cc_final: 0.8293 (mm) REVERT: C 241 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9141 (mm-30) REVERT: C 271 LEU cc_start: 0.9184 (mt) cc_final: 0.8982 (mt) REVERT: D 109 PHE cc_start: 0.8726 (m-10) cc_final: 0.8403 (m-80) REVERT: D 128 ASN cc_start: 0.8354 (t0) cc_final: 0.7893 (t0) REVERT: D 133 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8060 (tptp) REVERT: E 25 TRP cc_start: 0.8217 (p-90) cc_final: 0.7781 (p-90) REVERT: E 46 MET cc_start: 0.8202 (tpp) cc_final: 0.7967 (tpp) REVERT: E 70 MET cc_start: 0.8123 (mmp) cc_final: 0.7260 (mpp) outliers start: 0 outliers final: 0 residues processed: 726 average time/residue: 0.1326 time to fit residues: 147.7324 Evaluate side-chains 584 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** 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 645 GLN B 218 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096582 restraints weight = 42554.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100312 restraints weight = 21859.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102732 restraints weight = 13577.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104257 restraints weight = 9592.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105436 restraints weight = 7520.124| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17041 Z= 0.154 Angle : 0.602 11.270 23026 Z= 0.318 Chirality : 0.043 0.287 2464 Planarity : 0.004 0.057 2931 Dihedral : 8.488 136.923 2373 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % 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: 1.15 (0.15), residues: 1162 sheet: -0.37 (0.40), residues: 169 loop : 0.22 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 225 TYR 0.032 0.002 TYR C 169 PHE 0.029 0.002 PHE C 172 TRP 0.010 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (17038) covalent geometry : angle 0.59988 / 0.32 (23020) SS BOND : bond 0.00480 / 0.23 ( 3) SS BOND : angle 3.28903 / 1.62 ( 6) hydrogen bonds : bond 0.04056 / 2.63 ( 912) hydrogen bonds : angle 4.92554 / 3.42 ( 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 696 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 0.501 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: A 162 LYS cc_start: 0.9409 (tmtt) cc_final: 0.8953 (tmmt) REVERT: A 250 TYR cc_start: 0.8113 (m-80) cc_final: 0.7830 (m-80) REVERT: A 301 PHE cc_start: 0.9024 (m-80) cc_final: 0.8565 (m-80) REVERT: A 367 VAL cc_start: 0.9569 (m) cc_final: 0.9307 (p) REVERT: A 390 GLN cc_start: 0.8667 (mt0) cc_final: 0.8319 (mt0) REVERT: A 421 GLU cc_start: 0.8467 (pp20) cc_final: 0.8149 (pp20) REVERT: A 446 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8323 (mmm-85) REVERT: A 474 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 475 ASN cc_start: 0.8016 (m110) cc_final: 0.7714 (m110) REVERT: A 498 TYR cc_start: 0.8623 (m-80) cc_final: 0.8150 (m-80) REVERT: A 501 GLN cc_start: 0.9004 (tt0) cc_final: 0.8620 (tt0) REVERT: A 509 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8520 (tm-30) REVERT: A 515 ASP cc_start: 0.8868 (m-30) cc_final: 0.8408 (m-30) REVERT: A 558 TRP cc_start: 0.9073 (m100) cc_final: 0.8817 (m100) REVERT: A 615 MET cc_start: 0.8993 (mmm) cc_final: 0.8626 (mmm) REVERT: A 658 LEU cc_start: 0.9608 (mp) cc_final: 0.9259 (mp) REVERT: A 686 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7593 (mtp85) REVERT: B 27 ASP cc_start: 0.9496 (p0) cc_final: 0.9053 (p0) REVERT: B 87 LYS cc_start: 0.9093 (tppt) cc_final: 0.8476 (ttmt) REVERT: B 99 LYS cc_start: 0.9409 (tptm) cc_final: 0.9108 (tptm) REVERT: B 100 PHE cc_start: 0.9341 (t80) cc_final: 0.8689 (t80) REVERT: B 127 LEU cc_start: 0.9803 (mt) cc_final: 0.9499 (mm) REVERT: B 129 PHE cc_start: 0.9179 (m-80) cc_final: 0.8909 (m-80) REVERT: B 135 GLU cc_start: 0.8982 (mp0) cc_final: 0.8758 (pm20) REVERT: B 145 ILE cc_start: 0.9354 (tp) cc_final: 0.8950 (tp) REVERT: B 147 GLN cc_start: 0.8996 (mt0) cc_final: 0.8543 (mt0) REVERT: B 150 GLN cc_start: 0.9493 (tp40) cc_final: 0.8992 (tp-100) REVERT: B 190 MET cc_start: 0.9343 (mtm) cc_final: 0.8971 (mtm) REVERT: B 231 ASP cc_start: 0.8547 (t70) cc_final: 0.7840 (t70) REVERT: B 232 ASN cc_start: 0.9115 (m-40) cc_final: 0.8779 (m110) REVERT: B 235 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.7960 (mtm-85) REVERT: B 258 ILE cc_start: 0.9417 (tp) cc_final: 0.9211 (tp) REVERT: B 286 ASP cc_start: 0.8430 (m-30) cc_final: 0.8138 (m-30) REVERT: B 322 MET cc_start: 0.8481 (mmt) cc_final: 0.8188 (mmm) REVERT: B 348 MET cc_start: 0.9010 (ppp) cc_final: 0.8547 (ppp) REVERT: B 349 LEU cc_start: 0.9381 (mt) cc_final: 0.8705 (mt) REVERT: B 370 ASN cc_start: 0.9478 (m-40) cc_final: 0.9078 (m110) REVERT: B 378 PHE cc_start: 0.8957 (p90) cc_final: 0.8645 (p90) REVERT: B 402 GLU cc_start: 0.8118 (mp0) cc_final: 0.7470 (mp0) REVERT: B 415 ASN cc_start: 0.9045 (t0) cc_final: 0.8698 (t0) REVERT: B 446 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7177 (mmt-90) REVERT: B 475 ASN cc_start: 0.9145 (m-40) cc_final: 0.8869 (m110) REVERT: B 490 THR cc_start: 0.9267 (m) cc_final: 0.9002 (p) REVERT: B 493 MET cc_start: 0.9332 (tmm) cc_final: 0.8613 (tmm) REVERT: B 515 ASP cc_start: 0.8890 (m-30) cc_final: 0.8522 (p0) REVERT: B 526 GLU cc_start: 0.8874 (mp0) cc_final: 0.8622 (mp0) REVERT: B 550 MET cc_start: 0.8114 (mtp) cc_final: 0.7682 (mtp) REVERT: B 570 MET cc_start: 0.8615 (tpp) cc_final: 0.8327 (tpt) REVERT: B 574 TYR cc_start: 0.8421 (m-80) cc_final: 0.8021 (m-80) REVERT: B 612 TYR cc_start: 0.8244 (m-80) cc_final: 0.7766 (m-80) REVERT: B 656 LEU cc_start: 0.9276 (mt) cc_final: 0.9054 (mt) REVERT: B 687 THR cc_start: 0.9081 (p) cc_final: 0.8019 (m) REVERT: C 17 PHE cc_start: 0.8930 (p90) cc_final: 0.8221 (p90) REVERT: C 20 MET cc_start: 0.9246 (ppp) cc_final: 0.8989 (ppp) REVERT: C 21 PHE cc_start: 0.9022 (m-80) cc_final: 0.8456 (m-80) REVERT: C 46 TYR cc_start: 0.7729 (m-80) cc_final: 0.7423 (m-80) REVERT: C 68 GLU cc_start: 0.8982 (mp0) cc_final: 0.8733 (pm20) REVERT: C 74 MET cc_start: 0.9279 (mpp) cc_final: 0.9041 (mpp) REVERT: C 87 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8745 (ptpp) REVERT: C 89 VAL cc_start: 0.7641 (t) cc_final: 0.7298 (t) REVERT: C 95 MET cc_start: 0.8529 (ttp) cc_final: 0.8000 (ttp) REVERT: C 154 PHE cc_start: 0.9128 (t80) cc_final: 0.8909 (t80) REVERT: C 157 MET cc_start: 0.9450 (mtm) cc_final: 0.8937 (ptt) REVERT: C 174 TYR cc_start: 0.8668 (t80) cc_final: 0.8047 (t80) REVERT: C 212 ILE cc_start: 0.8652 (mt) cc_final: 0.8197 (mm) REVERT: C 226 GLU cc_start: 0.8976 (pt0) cc_final: 0.8708 (pt0) REVERT: C 239 GLU cc_start: 0.9027 (pt0) cc_final: 0.8668 (pt0) REVERT: C 277 PHE cc_start: 0.6780 (m-10) cc_final: 0.6472 (m-80) REVERT: D 128 ASN cc_start: 0.8308 (t0) cc_final: 0.7391 (t0) REVERT: D 133 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8043 (tptp) REVERT: D 242 TYR cc_start: 0.7739 (t80) cc_final: 0.7280 (t80) REVERT: E 25 TRP cc_start: 0.8257 (p-90) cc_final: 0.7589 (p-90) REVERT: E 46 MET cc_start: 0.8366 (tpp) cc_final: 0.8005 (tpp) REVERT: E 60 ASN cc_start: 0.9444 (t0) cc_final: 0.9231 (t0) outliers start: 2 outliers final: 1 residues processed: 694 average time/residue: 0.1319 time to fit residues: 140.1035 Evaluate side-chains 570 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 569 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 2.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094473 restraints weight = 42333.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098050 restraints weight = 21888.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100405 restraints weight = 13582.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101836 restraints weight = 9612.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102933 restraints weight = 7610.532| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17041 Z= 0.173 Angle : 0.628 11.608 23026 Z= 0.330 Chirality : 0.044 0.322 2464 Planarity : 0.004 0.039 2931 Dihedral : 8.557 138.491 2373 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2012 helix: 1.09 (0.15), residues: 1154 sheet: -0.46 (0.39), residues: 171 loop : 0.31 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.037 0.002 TYR C 130 PHE 0.039 0.002 PHE C 168 TRP 0.013 0.001 TRP A 623 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (17038) covalent geometry : angle 0.62385 / 0.33 (23020) SS BOND : bond 0.00670 / 0.33 ( 3) SS BOND : angle 4.65901 / 2.28 ( 6) hydrogen bonds : bond 0.04045 / 2.62 ( 912) hydrogen bonds : angle 4.96118 / 3.48 ( 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 693 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 692 time to evaluate : 0.653 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 45 THR cc_start: 0.9151 (t) cc_final: 0.8827 (t) REVERT: A 117 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8399 (mtp85) REVERT: A 145 ILE cc_start: 0.9252 (tp) cc_final: 0.9048 (tp) REVERT: A 147 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8088 (tp-100) REVERT: A 227 MET cc_start: 0.9295 (ptp) cc_final: 0.8946 (ptp) REVERT: A 228 LYS cc_start: 0.8986 (tptt) cc_final: 0.8588 (mptt) REVERT: A 250 TYR cc_start: 0.8066 (m-80) cc_final: 0.7761 (m-80) REVERT: A 301 PHE cc_start: 0.8923 (m-80) cc_final: 0.8618 (m-80) REVERT: A 322 MET cc_start: 0.7991 (mmm) cc_final: 0.7679 (mmm) REVERT: A 348 MET cc_start: 0.8902 (ptm) cc_final: 0.8664 (ptm) REVERT: A 367 VAL cc_start: 0.9585 (m) cc_final: 0.9349 (p) REVERT: A 421 GLU cc_start: 0.8533 (pp20) cc_final: 0.8132 (pp20) REVERT: A 474 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 475 ASN cc_start: 0.7928 (m110) cc_final: 0.7420 (m110) REVERT: A 498 TYR cc_start: 0.8727 (m-80) cc_final: 0.8283 (m-80) REVERT: A 501 GLN cc_start: 0.9044 (tt0) cc_final: 0.8589 (tt0) REVERT: A 509 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 515 ASP cc_start: 0.8885 (m-30) cc_final: 0.8442 (m-30) REVERT: A 558 TRP cc_start: 0.9084 (m100) cc_final: 0.8777 (m100) REVERT: A 615 MET cc_start: 0.9007 (mmm) cc_final: 0.8582 (mmm) REVERT: A 645 GLN cc_start: 0.8519 (tp40) cc_final: 0.7864 (tp40) REVERT: A 686 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7688 (mmm-85) REVERT: B 30 LYS cc_start: 0.9348 (tmtt) cc_final: 0.9123 (tptt) REVERT: B 99 LYS cc_start: 0.9416 (tptm) cc_final: 0.9097 (tptp) REVERT: B 100 PHE cc_start: 0.9273 (t80) cc_final: 0.9033 (t80) REVERT: B 120 ASP cc_start: 0.8682 (m-30) cc_final: 0.8453 (m-30) REVERT: B 127 LEU cc_start: 0.9785 (mt) cc_final: 0.9488 (mm) REVERT: B 129 PHE cc_start: 0.9145 (m-10) cc_final: 0.8863 (m-80) REVERT: B 135 GLU cc_start: 0.8972 (mp0) cc_final: 0.8741 (pm20) REVERT: B 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8055 (mm-40) REVERT: B 150 GLN cc_start: 0.9533 (tp40) cc_final: 0.8803 (tp-100) REVERT: B 184 ARG cc_start: 0.9488 (tpp80) cc_final: 0.8560 (tpp80) REVERT: B 186 ILE cc_start: 0.9565 (mt) cc_final: 0.9361 (mt) REVERT: B 190 MET cc_start: 0.9263 (mtm) cc_final: 0.9023 (mtm) REVERT: B 205 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7836 (mmmm) REVERT: B 227 MET cc_start: 0.9214 (mtp) cc_final: 0.8974 (mtp) REVERT: B 231 ASP cc_start: 0.8471 (t70) cc_final: 0.7186 (t70) REVERT: B 232 ASN cc_start: 0.9110 (m-40) cc_final: 0.8710 (m110) REVERT: B 235 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.7835 (mtm-85) REVERT: B 258 ILE cc_start: 0.9459 (tp) cc_final: 0.9194 (tp) REVERT: B 286 ASP cc_start: 0.8489 (m-30) cc_final: 0.8240 (m-30) REVERT: B 316 GLU cc_start: 0.9312 (tt0) cc_final: 0.9072 (tt0) REVERT: B 335 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 348 MET cc_start: 0.8971 (ppp) cc_final: 0.8507 (ppp) REVERT: B 349 LEU cc_start: 0.9347 (mt) cc_final: 0.8563 (mt) REVERT: B 370 ASN cc_start: 0.9528 (m-40) cc_final: 0.9126 (m110) REVERT: B 378 PHE cc_start: 0.8897 (p90) cc_final: 0.8520 (p90) REVERT: B 402 GLU cc_start: 0.8269 (mp0) cc_final: 0.7674 (mp0) REVERT: B 415 ASN cc_start: 0.9063 (t0) cc_final: 0.8739 (t0) REVERT: B 437 THR cc_start: 0.9564 (m) cc_final: 0.9203 (m) REVERT: B 475 ASN cc_start: 0.9172 (m-40) cc_final: 0.8884 (m110) REVERT: B 490 THR cc_start: 0.9445 (m) cc_final: 0.9199 (p) REVERT: B 515 ASP cc_start: 0.8909 (m-30) cc_final: 0.8562 (p0) REVERT: B 526 GLU cc_start: 0.8820 (mp0) cc_final: 0.8569 (mp0) REVERT: B 550 MET cc_start: 0.7933 (mtp) cc_final: 0.7619 (mtp) REVERT: B 574 TYR cc_start: 0.8460 (m-80) cc_final: 0.8018 (m-80) REVERT: B 575 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8467 (ptp90) REVERT: B 586 TYR cc_start: 0.9188 (m-80) cc_final: 0.8959 (m-80) REVERT: B 612 TYR cc_start: 0.8228 (m-80) cc_final: 0.7686 (m-80) REVERT: B 623 TRP cc_start: 0.8710 (t-100) cc_final: 0.7209 (t-100) REVERT: B 624 PHE cc_start: 0.7563 (m-10) cc_final: 0.7306 (m-10) REVERT: B 632 MET cc_start: 0.7605 (mtm) cc_final: 0.7210 (mtp) REVERT: B 656 LEU cc_start: 0.9293 (mt) cc_final: 0.9079 (mt) REVERT: C 17 PHE cc_start: 0.9027 (p90) cc_final: 0.8352 (p90) REVERT: C 20 MET cc_start: 0.9277 (ppp) cc_final: 0.9006 (ppp) REVERT: C 21 PHE cc_start: 0.9067 (m-80) cc_final: 0.8530 (m-80) REVERT: C 46 TYR cc_start: 0.7735 (m-80) cc_final: 0.7382 (m-80) REVERT: C 74 MET cc_start: 0.9328 (mpp) cc_final: 0.9035 (mpp) REVERT: C 87 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8720 (ptpp) REVERT: C 89 VAL cc_start: 0.7663 (t) cc_final: 0.7160 (t) REVERT: C 95 MET cc_start: 0.8499 (ttp) cc_final: 0.7804 (ttp) REVERT: C 174 TYR cc_start: 0.8947 (t80) cc_final: 0.8326 (t80) REVERT: C 179 TYR cc_start: 0.7935 (t80) cc_final: 0.7712 (t80) REVERT: C 212 ILE cc_start: 0.8622 (mt) cc_final: 0.8152 (tp) REVERT: C 231 LEU cc_start: 0.9189 (mt) cc_final: 0.8846 (mt) REVERT: C 277 PHE cc_start: 0.7055 (m-10) cc_final: 0.6822 (m-80) REVERT: D 25 ASN cc_start: 0.9450 (m-40) cc_final: 0.9246 (m-40) REVERT: D 35 ILE cc_start: 0.7157 (mm) cc_final: 0.6874 (mm) REVERT: D 42 LEU cc_start: 0.9179 (mp) cc_final: 0.8759 (mp) REVERT: D 54 THR cc_start: 0.5639 (m) cc_final: 0.5414 (p) REVERT: D 92 PHE cc_start: 0.6944 (t80) cc_final: 0.6634 (t80) REVERT: D 128 ASN cc_start: 0.8348 (t0) cc_final: 0.7441 (t0) REVERT: D 133 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8117 (tptp) REVERT: D 242 TYR cc_start: 0.7809 (t80) cc_final: 0.7380 (t80) REVERT: E 24 PHE cc_start: 0.8782 (m-80) cc_final: 0.8575 (m-80) REVERT: E 25 TRP cc_start: 0.8161 (p-90) cc_final: 0.7579 (p-90) REVERT: E 46 MET cc_start: 0.8241 (tpp) cc_final: 0.8003 (tpp) REVERT: E 67 TYR cc_start: 0.8564 (m-80) cc_final: 0.8267 (m-80) REVERT: E 70 MET cc_start: 0.7547 (mpp) cc_final: 0.5737 (mmt) outliers start: 1 outliers final: 0 residues processed: 692 average time/residue: 0.1291 time to fit residues: 137.6364 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 : 0.854 ------------------------------------------------------------------------------- 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: 7.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 365 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095663 restraints weight = 42517.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099272 restraints weight = 22104.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101564 restraints weight = 13796.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103152 restraints weight = 9863.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104129 restraints weight = 7722.336| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17041 Z= 0.146 Angle : 0.622 12.181 23026 Z= 0.324 Chirality : 0.043 0.264 2464 Planarity : 0.004 0.040 2931 Dihedral : 8.402 137.724 2373 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % 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: 0.99 (0.19), residues: 2012 helix: 1.12 (0.15), residues: 1145 sheet: -0.36 (0.40), residues: 165 loop : 0.36 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 686 TYR 0.031 0.002 TYR C 130 PHE 0.039 0.002 PHE C 168 TRP 0.010 0.001 TRP A 623 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17038) covalent geometry : angle 0.61721 / 0.32 (23020) SS BOND : bond 0.00367 / 0.19 ( 3) SS BOND : angle 4.59087 / 2.18 ( 6) hydrogen bonds : bond 0.03886 / 2.52 ( 912) hydrogen bonds : angle 4.96654 / 3.47 ( 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 677 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 676 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8913 (tptp) cc_final: 0.8582 (tppt) REVERT: A 113 LYS cc_start: 0.9502 (mmtt) cc_final: 0.9205 (mmmm) REVERT: A 117 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8350 (mtp85) REVERT: A 187 ASP cc_start: 0.8716 (t70) cc_final: 0.8360 (t0) REVERT: A 227 MET cc_start: 0.9261 (ptp) cc_final: 0.8996 (ptp) REVERT: A 228 LYS cc_start: 0.9059 (tptt) cc_final: 0.8589 (mptt) REVERT: A 230 LEU cc_start: 0.9742 (mt) cc_final: 0.9519 (mt) REVERT: A 250 TYR cc_start: 0.8173 (m-80) cc_final: 0.7849 (m-80) REVERT: A 254 PHE cc_start: 0.8707 (m-80) cc_final: 0.8396 (m-80) REVERT: A 257 ASP cc_start: 0.9026 (m-30) cc_final: 0.8788 (m-30) REVERT: A 301 PHE cc_start: 0.9007 (m-80) cc_final: 0.8681 (m-80) REVERT: A 338 ASN cc_start: 0.9498 (t0) cc_final: 0.9090 (t0) REVERT: A 367 VAL cc_start: 0.9571 (m) cc_final: 0.9347 (p) REVERT: A 390 GLN cc_start: 0.8713 (mt0) cc_final: 0.8502 (mt0) REVERT: A 418 ASN cc_start: 0.9369 (m-40) cc_final: 0.8595 (m110) REVERT: A 474 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 475 ASN cc_start: 0.7952 (m110) cc_final: 0.7367 (m110) REVERT: A 491 PHE cc_start: 0.9524 (t80) cc_final: 0.9054 (t80) REVERT: A 498 TYR cc_start: 0.8699 (m-80) cc_final: 0.8253 (m-80) REVERT: A 501 GLN cc_start: 0.9021 (tt0) cc_final: 0.8705 (tt0) REVERT: A 515 ASP cc_start: 0.8855 (m-30) cc_final: 0.8410 (m-30) REVERT: A 595 MET cc_start: 0.8887 (mmm) cc_final: 0.8548 (mmp) REVERT: A 615 MET cc_start: 0.8973 (mmm) cc_final: 0.8564 (mmm) REVERT: A 645 GLN cc_start: 0.8543 (tp40) cc_final: 0.8103 (tp-100) REVERT: A 668 ASN cc_start: 0.9253 (m-40) cc_final: 0.8877 (p0) REVERT: A 686 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7825 (mtp180) REVERT: B 30 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9126 (tptt) REVERT: B 87 LYS cc_start: 0.9042 (tppt) cc_final: 0.8462 (ttmt) REVERT: B 99 LYS cc_start: 0.9446 (tptm) cc_final: 0.9211 (tptm) REVERT: B 100 PHE cc_start: 0.9213 (t80) cc_final: 0.8991 (t80) REVERT: B 127 LEU cc_start: 0.9782 (mt) cc_final: 0.9462 (mm) REVERT: B 129 PHE cc_start: 0.9141 (m-10) cc_final: 0.8851 (m-80) REVERT: B 135 GLU cc_start: 0.8919 (mp0) cc_final: 0.8707 (pm20) REVERT: B 145 ILE cc_start: 0.9375 (tp) cc_final: 0.8983 (tp) REVERT: B 147 GLN cc_start: 0.9099 (mt0) cc_final: 0.8047 (mm-40) REVERT: B 150 GLN cc_start: 0.9520 (tp40) cc_final: 0.9273 (tp-100) REVERT: B 184 ARG cc_start: 0.9482 (tpp80) cc_final: 0.8642 (tpp80) REVERT: B 231 ASP cc_start: 0.8489 (t70) cc_final: 0.7285 (t70) REVERT: B 232 ASN cc_start: 0.9082 (m-40) cc_final: 0.8710 (m110) REVERT: B 235 ARG cc_start: 0.8818 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: B 240 MET cc_start: 0.7667 (ppp) cc_final: 0.7274 (ppp) REVERT: B 258 ILE cc_start: 0.9446 (tp) cc_final: 0.9175 (tp) REVERT: B 316 GLU cc_start: 0.9299 (tt0) cc_final: 0.9086 (tt0) REVERT: B 348 MET cc_start: 0.8957 (ppp) cc_final: 0.8438 (ppp) REVERT: B 349 LEU cc_start: 0.9343 (mt) cc_final: 0.8566 (mt) REVERT: B 370 ASN cc_start: 0.9486 (m-40) cc_final: 0.9075 (m110) REVERT: B 375 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8425 (mmmm) REVERT: B 378 PHE cc_start: 0.8889 (p90) cc_final: 0.8457 (p90) REVERT: B 402 GLU cc_start: 0.8310 (mp0) cc_final: 0.7647 (mp0) REVERT: B 415 ASN cc_start: 0.9012 (t0) cc_final: 0.8725 (t0) REVERT: B 426 GLU cc_start: 0.8890 (tp30) cc_final: 0.8095 (tp30) REVERT: B 437 THR cc_start: 0.9505 (m) cc_final: 0.9170 (m) REVERT: B 475 ASN cc_start: 0.9152 (m-40) cc_final: 0.8884 (m110) REVERT: B 490 THR cc_start: 0.9436 (m) cc_final: 0.9163 (p) REVERT: B 515 ASP cc_start: 0.8900 (m-30) cc_final: 0.8572 (p0) REVERT: B 526 GLU cc_start: 0.8857 (mp0) cc_final: 0.8594 (mp0) REVERT: B 550 MET cc_start: 0.7964 (mtp) cc_final: 0.7754 (mtp) REVERT: B 570 MET cc_start: 0.8318 (tpp) cc_final: 0.8069 (tpt) REVERT: B 574 TYR cc_start: 0.8422 (m-80) cc_final: 0.7989 (m-80) REVERT: B 575 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8550 (ptp90) REVERT: B 586 TYR cc_start: 0.9158 (m-80) cc_final: 0.8887 (m-80) REVERT: B 612 TYR cc_start: 0.8380 (m-80) cc_final: 0.8170 (m-80) REVERT: B 623 TRP cc_start: 0.8733 (t-100) cc_final: 0.8122 (t-100) REVERT: B 656 LEU cc_start: 0.9301 (mt) cc_final: 0.9089 (mt) REVERT: C 17 PHE cc_start: 0.9032 (p90) cc_final: 0.8314 (p90) REVERT: C 20 MET cc_start: 0.9289 (ppp) cc_final: 0.9017 (ppp) REVERT: C 21 PHE cc_start: 0.9054 (m-80) cc_final: 0.8516 (m-80) REVERT: C 46 TYR cc_start: 0.7727 (m-80) cc_final: 0.7336 (m-80) REVERT: C 74 MET cc_start: 0.9338 (mpp) cc_final: 0.9043 (mpp) REVERT: C 87 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8724 (ptpp) REVERT: C 89 VAL cc_start: 0.7754 (t) cc_final: 0.7176 (t) REVERT: C 95 MET cc_start: 0.8559 (ttp) cc_final: 0.7768 (ttp) REVERT: C 157 MET cc_start: 0.9319 (mtm) cc_final: 0.8922 (ptm) REVERT: C 174 TYR cc_start: 0.8959 (t80) cc_final: 0.7598 (t80) REVERT: C 178 PHE cc_start: 0.9050 (m-10) cc_final: 0.8716 (m-10) REVERT: C 231 LEU cc_start: 0.9132 (mt) cc_final: 0.8892 (mt) REVERT: C 277 PHE cc_start: 0.7038 (m-10) cc_final: 0.6826 (m-80) REVERT: C 315 LEU cc_start: 0.8450 (mt) cc_final: 0.7453 (mt) REVERT: D 54 THR cc_start: 0.5573 (m) cc_final: 0.5361 (p) REVERT: D 92 PHE cc_start: 0.6971 (t80) cc_final: 0.6481 (t80) REVERT: D 96 MET cc_start: 0.7795 (tpt) cc_final: 0.7442 (tpt) REVERT: D 128 ASN cc_start: 0.8324 (t0) cc_final: 0.7319 (t0) REVERT: D 242 TYR cc_start: 0.7776 (t80) cc_final: 0.7301 (t80) REVERT: E 25 TRP cc_start: 0.8139 (p-90) cc_final: 0.7574 (p-90) REVERT: E 41 GLU cc_start: 0.8811 (pt0) cc_final: 0.8581 (tm-30) REVERT: E 46 MET cc_start: 0.8316 (tpp) cc_final: 0.8028 (tpp) REVERT: E 67 TYR cc_start: 0.8698 (m-80) cc_final: 0.8468 (m-80) REVERT: E 93 LYS cc_start: 0.7725 (tptp) cc_final: 0.6916 (tptt) outliers start: 1 outliers final: 1 residues processed: 677 average time/residue: 0.1348 time to fit residues: 139.2935 Evaluate side-chains 574 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 573 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 6.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** 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 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098248 restraints weight = 42770.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101714 restraints weight = 22480.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103934 restraints weight = 14069.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105480 restraints weight = 10074.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106424 restraints weight = 7905.605| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17041 Z= 0.153 Angle : 0.628 11.822 23026 Z= 0.329 Chirality : 0.043 0.205 2464 Planarity : 0.004 0.043 2931 Dihedral : 8.257 138.590 2373 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.94 (0.19), residues: 2012 helix: 1.11 (0.15), residues: 1147 sheet: -0.35 (0.39), residues: 165 loop : 0.27 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 485 TYR 0.029 0.002 TYR C 130 PHE 0.031 0.002 PHE A 234 TRP 0.012 0.001 TRP A 623 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17038) covalent geometry : angle 0.62418 / 0.33 (23020) SS BOND : bond 0.01009 / 0.49 ( 3) SS BOND : angle 4.11539 / 2.00 ( 6) hydrogen bonds : bond 0.03834 / 2.49 ( 912) hydrogen bonds : angle 5.03250 / 3.53 ( 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 675 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 0.691 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: 0.8925 (tptp) cc_final: 0.8636 (tppt) REVERT: A 113 LYS cc_start: 0.9490 (mmtt) cc_final: 0.9174 (mmmm) REVERT: A 147 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8440 (tp40) REVERT: A 162 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8857 (ttpt) REVERT: A 181 ASP cc_start: 0.8697 (m-30) cc_final: 0.8493 (m-30) REVERT: A 187 ASP cc_start: 0.8749 (t70) cc_final: 0.8393 (t0) REVERT: A 227 MET cc_start: 0.9304 (ptp) cc_final: 0.9025 (ptp) REVERT: A 228 LYS cc_start: 0.9042 (tptt) cc_final: 0.8580 (tptt) REVERT: A 230 LEU cc_start: 0.9717 (mt) cc_final: 0.9465 (mt) REVERT: A 234 PHE cc_start: 0.9424 (m-80) cc_final: 0.9199 (m-80) REVERT: A 250 TYR cc_start: 0.8220 (m-80) cc_final: 0.7879 (m-80) REVERT: A 301 PHE cc_start: 0.8939 (m-80) cc_final: 0.8642 (m-80) REVERT: A 367 VAL cc_start: 0.9597 (m) cc_final: 0.9377 (p) REVERT: A 390 GLN cc_start: 0.8810 (mt0) cc_final: 0.8591 (mt0) REVERT: A 418 ASN cc_start: 0.8986 (m-40) cc_final: 0.8604 (m-40) REVERT: A 471 TYR cc_start: 0.8550 (t80) cc_final: 0.7984 (t80) REVERT: A 474 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 491 PHE cc_start: 0.9527 (t80) cc_final: 0.9201 (t80) REVERT: A 498 TYR cc_start: 0.8762 (m-80) cc_final: 0.8410 (m-80) REVERT: A 501 GLN cc_start: 0.8997 (tt0) cc_final: 0.8493 (tm-30) REVERT: A 515 ASP cc_start: 0.8878 (m-30) cc_final: 0.8435 (m-30) REVERT: A 590 SER cc_start: 0.9444 (p) cc_final: 0.9012 (p) REVERT: A 595 MET cc_start: 0.8888 (mmm) cc_final: 0.8685 (mmp) REVERT: A 615 MET cc_start: 0.8960 (mmm) cc_final: 0.8571 (mmm) REVERT: A 645 GLN cc_start: 0.8637 (tp40) cc_final: 0.8099 (tp-100) REVERT: A 655 THR cc_start: 0.9001 (m) cc_final: 0.8687 (m) REVERT: A 686 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7719 (mmm-85) REVERT: B 30 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9118 (tptt) REVERT: B 87 LYS cc_start: 0.9047 (tppt) cc_final: 0.8414 (tptp) REVERT: B 99 LYS cc_start: 0.9439 (tptm) cc_final: 0.9227 (tptm) REVERT: B 117 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: B 127 LEU cc_start: 0.9778 (mt) cc_final: 0.9478 (mm) REVERT: B 129 PHE cc_start: 0.9130 (m-10) cc_final: 0.8873 (m-80) REVERT: B 138 LYS cc_start: 0.9406 (mtpt) cc_final: 0.9062 (mtmm) REVERT: B 147 GLN cc_start: 0.9154 (mt0) cc_final: 0.8301 (mt0) REVERT: B 184 ARG cc_start: 0.9510 (tpp80) cc_final: 0.9089 (tpp80) REVERT: B 231 ASP cc_start: 0.8480 (t70) cc_final: 0.7136 (t70) REVERT: B 232 ASN cc_start: 0.9055 (m-40) cc_final: 0.8526 (m110) REVERT: B 235 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: B 240 MET cc_start: 0.7733 (ppp) cc_final: 0.7294 (ppp) REVERT: B 258 ILE cc_start: 0.9435 (tp) cc_final: 0.9152 (tp) REVERT: B 286 ASP cc_start: 0.8533 (m-30) cc_final: 0.8110 (m-30) REVERT: B 316 GLU cc_start: 0.9304 (tt0) cc_final: 0.9006 (tt0) REVERT: B 335 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 348 MET cc_start: 0.8971 (ppp) cc_final: 0.8410 (ppp) REVERT: B 349 LEU cc_start: 0.9343 (mt) cc_final: 0.8611 (mt) REVERT: B 370 ASN cc_start: 0.9485 (m-40) cc_final: 0.9062 (m110) REVERT: B 378 PHE cc_start: 0.8843 (p90) cc_final: 0.8425 (p90) REVERT: B 402 GLU cc_start: 0.8343 (mp0) cc_final: 0.7693 (mp0) REVERT: B 437 THR cc_start: 0.9494 (m) cc_final: 0.9149 (m) REVERT: B 490 THR cc_start: 0.9425 (m) cc_final: 0.9157 (p) REVERT: B 515 ASP cc_start: 0.8899 (m-30) cc_final: 0.8589 (p0) REVERT: B 526 GLU cc_start: 0.8842 (mp0) cc_final: 0.8633 (mp0) REVERT: B 546 LEU cc_start: 0.9290 (mp) cc_final: 0.9013 (mp) REVERT: B 570 MET cc_start: 0.8654 (tpp) cc_final: 0.8385 (tpp) REVERT: B 574 TYR cc_start: 0.8445 (m-80) cc_final: 0.7945 (m-80) REVERT: B 575 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8540 (ptp90) REVERT: B 623 TRP cc_start: 0.8762 (t-100) cc_final: 0.7448 (t-100) REVERT: B 656 LEU cc_start: 0.9253 (mt) cc_final: 0.9033 (mt) REVERT: C 17 PHE cc_start: 0.9030 (p90) cc_final: 0.8344 (p90) REVERT: C 20 MET cc_start: 0.9406 (ppp) cc_final: 0.9171 (ppp) REVERT: C 21 PHE cc_start: 0.9100 (m-80) cc_final: 0.8549 (m-80) REVERT: C 46 TYR cc_start: 0.7706 (m-80) cc_final: 0.7312 (m-80) REVERT: C 56 MET cc_start: 0.0280 (ptm) cc_final: -0.0055 (ttm) REVERT: C 74 MET cc_start: 0.9331 (mpp) cc_final: 0.9071 (mpp) REVERT: C 87 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8695 (ptpp) REVERT: C 89 VAL cc_start: 0.7601 (t) cc_final: 0.7032 (t) REVERT: C 95 MET cc_start: 0.8431 (ttp) cc_final: 0.7751 (ttp) REVERT: C 157 MET cc_start: 0.9336 (mtm) cc_final: 0.9010 (ptp) REVERT: C 174 TYR cc_start: 0.8963 (t80) cc_final: 0.8205 (t80) REVERT: C 231 LEU cc_start: 0.9138 (mt) cc_final: 0.8906 (mt) REVERT: C 239 GLU cc_start: 0.8950 (pt0) cc_final: 0.8479 (pt0) REVERT: D 25 ASN cc_start: 0.9388 (m-40) cc_final: 0.8991 (m-40) REVERT: D 96 MET cc_start: 0.7902 (tpt) cc_final: 0.7653 (tpt) REVERT: D 128 ASN cc_start: 0.8373 (t0) cc_final: 0.7367 (t0) REVERT: D 242 TYR cc_start: 0.7781 (t80) cc_final: 0.7293 (t80) REVERT: D 315 LEU cc_start: 0.9088 (mm) cc_final: 0.8888 (mt) REVERT: E 24 PHE cc_start: 0.9250 (m-10) cc_final: 0.8838 (m-80) REVERT: E 25 TRP cc_start: 0.8216 (p-90) cc_final: 0.7556 (p-90) REVERT: E 46 MET cc_start: 0.8346 (tpp) cc_final: 0.8032 (tpp) REVERT: E 67 TYR cc_start: 0.8771 (m-80) cc_final: 0.8442 (m-80) REVERT: E 70 MET cc_start: 0.7990 (mpp) cc_final: 0.6595 (mmp) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.1322 time to fit residues: 136.8555 Evaluate side-chains 565 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 0.7980 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** 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 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098986 restraints weight = 43060.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102563 restraints weight = 22779.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.104871 restraints weight = 14332.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106332 restraints weight = 10285.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107448 restraints weight = 8174.578| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 17041 Z= 0.138 Angle : 0.629 11.636 23026 Z= 0.330 Chirality : 0.044 0.289 2464 Planarity : 0.004 0.045 2931 Dihedral : 8.089 138.029 2373 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1143 sheet: -0.31 (0.41), residues: 157 loop : 0.15 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 686 TYR 0.026 0.002 TYR B 630 PHE 0.041 0.002 PHE C 172 TRP 0.010 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17038) covalent geometry : angle 0.62448 / 0.33 (23020) SS BOND : bond 0.00288 / 0.15 ( 3) SS BOND : angle 4.82938 / 2.27 ( 6) hydrogen bonds : bond 0.03785 / 2.46 ( 912) hydrogen bonds : angle 5.06327 / 3.55 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.675 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: 0.8957 (tptp) cc_final: 0.8699 (tppt) REVERT: A 113 LYS cc_start: 0.9472 (mmtt) cc_final: 0.9150 (mmmm) REVERT: A 147 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8360 (tp-100) REVERT: A 227 MET cc_start: 0.9313 (ptp) cc_final: 0.9036 (ptp) REVERT: A 228 LYS cc_start: 0.9058 (tptt) cc_final: 0.8578 (tptt) REVERT: A 230 LEU cc_start: 0.9730 (mt) cc_final: 0.9452 (mt) REVERT: A 234 PHE cc_start: 0.9374 (m-80) cc_final: 0.9120 (m-80) REVERT: A 250 TYR cc_start: 0.8210 (m-80) cc_final: 0.7870 (m-80) REVERT: A 262 LEU cc_start: 0.9566 (mt) cc_final: 0.9272 (mt) REVERT: A 290 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 291 LEU cc_start: 0.9476 (mm) cc_final: 0.9021 (mm) REVERT: A 301 PHE cc_start: 0.8927 (m-80) cc_final: 0.8668 (m-80) REVERT: A 338 ASN cc_start: 0.9344 (t0) cc_final: 0.8286 (t0) REVERT: A 367 VAL cc_start: 0.9606 (m) cc_final: 0.9393 (p) REVERT: A 390 GLN cc_start: 0.8857 (mt0) cc_final: 0.8607 (mt0) REVERT: A 417 LEU cc_start: 0.9221 (tp) cc_final: 0.8711 (tp) REVERT: A 418 ASN cc_start: 0.8942 (m-40) cc_final: 0.8493 (m-40) REVERT: A 471 TYR cc_start: 0.8448 (t80) cc_final: 0.7963 (t80) REVERT: A 474 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 494 MET cc_start: 0.8596 (mmp) cc_final: 0.8353 (mmp) REVERT: A 501 GLN cc_start: 0.8985 (tt0) cc_final: 0.8465 (tm-30) REVERT: A 515 ASP cc_start: 0.8858 (m-30) cc_final: 0.8449 (m-30) REVERT: A 570 MET cc_start: 0.8166 (ptm) cc_final: 0.7895 (ptm) REVERT: A 595 MET cc_start: 0.8909 (mmm) cc_final: 0.8706 (mmp) REVERT: A 615 MET cc_start: 0.8942 (mmm) cc_final: 0.8544 (mmm) REVERT: A 645 GLN cc_start: 0.8689 (tp40) cc_final: 0.8341 (tp-100) REVERT: A 668 ASN cc_start: 0.9275 (m-40) cc_final: 0.8872 (p0) REVERT: A 686 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7862 (mtp180) REVERT: B 30 LYS cc_start: 0.9337 (tmtt) cc_final: 0.9105 (tptt) REVERT: B 64 TYR cc_start: 0.8685 (m-10) cc_final: 0.8435 (m-10) REVERT: B 87 LYS cc_start: 0.9006 (tppt) cc_final: 0.8406 (tptp) REVERT: B 99 LYS cc_start: 0.9473 (tptm) cc_final: 0.9249 (tptm) REVERT: B 127 LEU cc_start: 0.9777 (mt) cc_final: 0.9480 (mm) REVERT: B 129 PHE cc_start: 0.9122 (m-10) cc_final: 0.8866 (m-80) REVERT: B 138 LYS cc_start: 0.9397 (mtpt) cc_final: 0.9047 (mtmm) REVERT: B 147 GLN cc_start: 0.9215 (mt0) cc_final: 0.8136 (mt0) REVERT: B 184 ARG cc_start: 0.9494 (tpp80) cc_final: 0.9000 (tpp80) REVERT: B 190 MET cc_start: 0.9395 (mtm) cc_final: 0.8970 (mtm) REVERT: B 202 ASN cc_start: 0.8533 (t0) cc_final: 0.7666 (t0) REVERT: B 228 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9195 (mmmt) REVERT: B 231 ASP cc_start: 0.8480 (t70) cc_final: 0.7220 (t70) REVERT: B 232 ASN cc_start: 0.9047 (m-40) cc_final: 0.8452 (m110) REVERT: B 235 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.7855 (mtm-85) REVERT: B 251 LEU cc_start: 0.9104 (tp) cc_final: 0.8902 (tp) REVERT: B 258 ILE cc_start: 0.9423 (tp) cc_final: 0.9150 (tp) REVERT: B 286 ASP cc_start: 0.8573 (m-30) cc_final: 0.8268 (m-30) REVERT: B 316 GLU cc_start: 0.9290 (tt0) cc_final: 0.8970 (tt0) REVERT: B 335 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 348 MET cc_start: 0.8993 (ppp) cc_final: 0.8462 (ppp) REVERT: B 349 LEU cc_start: 0.9308 (mt) cc_final: 0.8612 (mt) REVERT: B 370 ASN cc_start: 0.9521 (m-40) cc_final: 0.9090 (m110) REVERT: B 375 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8427 (mmmm) REVERT: B 402 GLU cc_start: 0.8323 (mp0) cc_final: 0.7657 (mp0) REVERT: B 415 ASN cc_start: 0.9149 (t0) cc_final: 0.8442 (t0) REVERT: B 418 ASN cc_start: 0.9003 (m-40) cc_final: 0.8462 (m-40) REVERT: B 437 THR cc_start: 0.9478 (m) cc_final: 0.9155 (m) REVERT: B 490 THR cc_start: 0.9421 (m) cc_final: 0.9139 (p) REVERT: B 515 ASP cc_start: 0.8744 (m-30) cc_final: 0.8538 (p0) REVERT: B 550 MET cc_start: 0.7923 (mtp) cc_final: 0.7493 (mtt) REVERT: B 570 MET cc_start: 0.8889 (tpp) cc_final: 0.8393 (tpt) REVERT: B 574 TYR cc_start: 0.8546 (m-80) cc_final: 0.8084 (m-80) REVERT: B 612 TYR cc_start: 0.8414 (m-80) cc_final: 0.8156 (m-80) REVERT: B 623 TRP cc_start: 0.8810 (t-100) cc_final: 0.8318 (t-100) REVERT: B 632 MET cc_start: 0.7294 (mtm) cc_final: 0.7039 (ptp) REVERT: B 656 LEU cc_start: 0.9270 (mt) cc_final: 0.9061 (mt) REVERT: C 17 PHE cc_start: 0.9037 (p90) cc_final: 0.8342 (p90) REVERT: C 20 MET cc_start: 0.9435 (ppp) cc_final: 0.9213 (ppp) REVERT: C 21 PHE cc_start: 0.9110 (m-80) cc_final: 0.8542 (m-80) REVERT: C 46 TYR cc_start: 0.7800 (m-80) cc_final: 0.7424 (m-80) REVERT: C 56 MET cc_start: 0.0357 (ptm) cc_final: -0.0352 (ttm) REVERT: C 74 MET cc_start: 0.9345 (mpp) cc_final: 0.9066 (mpp) REVERT: C 87 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8690 (ptpp) REVERT: C 89 VAL cc_start: 0.7605 (t) cc_final: 0.7087 (t) REVERT: C 95 MET cc_start: 0.8523 (ttp) cc_final: 0.7656 (ttp) REVERT: C 157 MET cc_start: 0.9462 (mtm) cc_final: 0.8948 (ptp) REVERT: C 174 TYR cc_start: 0.8959 (t80) cc_final: 0.7635 (t80) REVERT: C 178 PHE cc_start: 0.9079 (m-10) cc_final: 0.8616 (m-10) REVERT: C 179 TYR cc_start: 0.7858 (t80) cc_final: 0.7609 (t80) REVERT: C 231 LEU cc_start: 0.9135 (mt) cc_final: 0.8915 (mt) REVERT: C 239 GLU cc_start: 0.8795 (pt0) cc_final: 0.8312 (pt0) REVERT: C 274 ASP cc_start: 0.8436 (p0) cc_final: 0.8034 (p0) REVERT: C 315 LEU cc_start: 0.8480 (mt) cc_final: 0.7288 (mt) REVERT: D 25 ASN cc_start: 0.9391 (m-40) cc_final: 0.8895 (m-40) REVERT: D 92 PHE cc_start: 0.7026 (t80) cc_final: 0.6061 (t80) REVERT: D 128 ASN cc_start: 0.8402 (t0) cc_final: 0.7427 (t0) REVERT: D 242 TYR cc_start: 0.7759 (t80) cc_final: 0.7273 (t80) REVERT: E 24 PHE cc_start: 0.9248 (m-10) cc_final: 0.8878 (m-80) REVERT: E 25 TRP cc_start: 0.8253 (p-90) cc_final: 0.7545 (p-90) REVERT: E 42 LEU cc_start: 0.8119 (mt) cc_final: 0.7909 (mt) REVERT: E 46 MET cc_start: 0.8347 (tpp) cc_final: 0.8067 (tpp) REVERT: E 67 TYR cc_start: 0.8787 (m-80) cc_final: 0.8424 (m-80) REVERT: E 70 MET cc_start: 0.8031 (mpp) cc_final: 0.7599 (mpp) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1319 time to fit residues: 133.6013 Evaluate side-chains 578 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 588 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101415 restraints weight = 42946.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104667 restraints weight = 23205.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106828 restraints weight = 14957.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108352 restraints weight = 10680.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109241 restraints weight = 8389.831| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17041 Z= 0.158 Angle : 0.656 11.529 23026 Z= 0.344 Chirality : 0.044 0.238 2464 Planarity : 0.004 0.048 2931 Dihedral : 8.009 139.312 2373 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.73 (0.19), residues: 2012 helix: 0.99 (0.15), residues: 1138 sheet: -0.13 (0.41), residues: 161 loop : -0.02 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.026 0.002 TYR C 130 PHE 0.038 0.002 PHE C 172 TRP 0.014 0.002 TRP A 623 HIS 0.007 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (17038) covalent geometry : angle 0.65163 / 0.34 (23020) SS BOND : bond 0.00579 / 0.28 ( 3) SS BOND : angle 4.78538 / 2.27 ( 6) hydrogen bonds : bond 0.03812 / 2.47 ( 912) hydrogen bonds : angle 5.03919 / 3.53 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 0.418 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: A 8 LYS cc_start: 0.8937 (tptp) cc_final: 0.8700 (tppt) REVERT: A 113 LYS cc_start: 0.9463 (mmtt) cc_final: 0.9147 (mmmm) REVERT: A 147 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8417 (tp40) REVERT: A 184 ARG cc_start: 0.9371 (mmm-85) cc_final: 0.9150 (mmm160) REVERT: A 191 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8486 (mp10) REVERT: A 209 LYS cc_start: 0.9310 (tttm) cc_final: 0.9093 (tttm) REVERT: A 227 MET cc_start: 0.9289 (ptp) cc_final: 0.9025 (ptp) REVERT: A 228 LYS cc_start: 0.9050 (tptt) cc_final: 0.8564 (tptt) REVERT: A 230 LEU cc_start: 0.9703 (mt) cc_final: 0.9437 (mt) REVERT: A 250 TYR cc_start: 0.8275 (m-80) cc_final: 0.7904 (m-80) REVERT: A 254 PHE cc_start: 0.8673 (m-80) cc_final: 0.8356 (m-80) REVERT: A 290 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 291 LEU cc_start: 0.9457 (mm) cc_final: 0.8927 (mm) REVERT: A 301 PHE cc_start: 0.8953 (m-80) cc_final: 0.8606 (m-80) REVERT: A 358 ILE cc_start: 0.9269 (mm) cc_final: 0.8998 (mm) REVERT: A 367 VAL cc_start: 0.9588 (m) cc_final: 0.9378 (p) REVERT: A 390 GLN cc_start: 0.8855 (mt0) cc_final: 0.8627 (mt0) REVERT: A 418 ASN cc_start: 0.8950 (m-40) cc_final: 0.8489 (m110) REVERT: A 446 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7993 (tpp-160) REVERT: A 471 TYR cc_start: 0.8562 (t80) cc_final: 0.8039 (t80) REVERT: A 474 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 501 GLN cc_start: 0.8991 (tt0) cc_final: 0.8467 (tt0) REVERT: A 515 ASP cc_start: 0.8857 (m-30) cc_final: 0.8446 (m-30) REVERT: A 570 MET cc_start: 0.8284 (ptm) cc_final: 0.7849 (ptt) REVERT: A 590 SER cc_start: 0.9434 (t) cc_final: 0.9182 (p) REVERT: A 615 MET cc_start: 0.8928 (mmm) cc_final: 0.8527 (mmm) REVERT: A 645 GLN cc_start: 0.8756 (tp40) cc_final: 0.8550 (tp-100) REVERT: B 30 LYS cc_start: 0.9330 (tmtt) cc_final: 0.9101 (tptt) REVERT: B 87 LYS cc_start: 0.9004 (tppt) cc_final: 0.8460 (tptp) REVERT: B 100 PHE cc_start: 0.9155 (t80) cc_final: 0.8922 (t80) REVERT: B 109 ASN cc_start: 0.8895 (m-40) cc_final: 0.8513 (p0) REVERT: B 120 ASP cc_start: 0.8866 (m-30) cc_final: 0.8660 (m-30) REVERT: B 127 LEU cc_start: 0.9776 (mt) cc_final: 0.9481 (mm) REVERT: B 129 PHE cc_start: 0.9082 (m-10) cc_final: 0.8822 (m-80) REVERT: B 138 LYS cc_start: 0.9402 (mtpt) cc_final: 0.9063 (mttt) REVERT: B 147 GLN cc_start: 0.9150 (mt0) cc_final: 0.7998 (mt0) REVERT: B 150 GLN cc_start: 0.9308 (tp-100) cc_final: 0.9067 (tp-100) REVERT: B 184 ARG cc_start: 0.9504 (tpp80) cc_final: 0.9120 (tpp80) REVERT: B 186 ILE cc_start: 0.9553 (mt) cc_final: 0.9305 (mt) REVERT: B 190 MET cc_start: 0.9350 (mtm) cc_final: 0.8920 (mtm) REVERT: B 231 ASP cc_start: 0.8512 (t70) cc_final: 0.7206 (t70) REVERT: B 232 ASN cc_start: 0.9061 (m-40) cc_final: 0.8474 (m110) REVERT: B 235 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: B 258 ILE cc_start: 0.9456 (tp) cc_final: 0.9153 (tp) REVERT: B 316 GLU cc_start: 0.9300 (tt0) cc_final: 0.9047 (tt0) REVERT: B 343 LEU cc_start: 0.9714 (mt) cc_final: 0.9511 (mm) REVERT: B 348 MET cc_start: 0.8987 (ppp) cc_final: 0.8441 (ppp) REVERT: B 349 LEU cc_start: 0.9310 (mt) cc_final: 0.8586 (mt) REVERT: B 370 ASN cc_start: 0.9528 (m-40) cc_final: 0.9082 (m110) REVERT: B 378 PHE cc_start: 0.8928 (p90) cc_final: 0.8455 (p90) REVERT: B 402 GLU cc_start: 0.8379 (mp0) cc_final: 0.7731 (mp0) REVERT: B 427 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8822 (pttm) REVERT: B 437 THR cc_start: 0.9481 (m) cc_final: 0.9144 (m) REVERT: B 490 THR cc_start: 0.9414 (m) cc_final: 0.9176 (p) REVERT: B 570 MET cc_start: 0.8909 (tpp) cc_final: 0.8427 (tpt) REVERT: B 574 TYR cc_start: 0.8566 (m-80) cc_final: 0.8109 (m-80) REVERT: B 588 GLN cc_start: 0.8479 (mm110) cc_final: 0.7414 (mm110) REVERT: B 612 TYR cc_start: 0.8377 (m-80) cc_final: 0.7720 (m-80) REVERT: B 623 TRP cc_start: 0.8776 (t-100) cc_final: 0.8296 (t-100) REVERT: B 656 LEU cc_start: 0.9239 (mt) cc_final: 0.9003 (mt) REVERT: C 17 PHE cc_start: 0.9057 (p90) cc_final: 0.8336 (p90) REVERT: C 20 MET cc_start: 0.9429 (ppp) cc_final: 0.9188 (ppp) REVERT: C 21 PHE cc_start: 0.9121 (m-80) cc_final: 0.8562 (m-80) REVERT: C 46 TYR cc_start: 0.7815 (m-80) cc_final: 0.7426 (m-80) REVERT: C 56 MET cc_start: 0.0589 (ptm) cc_final: -0.0038 (ttm) REVERT: C 68 GLU cc_start: 0.8988 (mp0) cc_final: 0.8614 (pm20) REVERT: C 74 MET cc_start: 0.9322 (mpp) cc_final: 0.9078 (mpp) REVERT: C 87 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8717 (ptpp) REVERT: C 89 VAL cc_start: 0.7569 (t) cc_final: 0.7070 (t) REVERT: C 95 MET cc_start: 0.8502 (ttp) cc_final: 0.7765 (ttp) REVERT: C 157 MET cc_start: 0.9401 (mtm) cc_final: 0.8874 (ptp) REVERT: C 174 TYR cc_start: 0.8927 (t80) cc_final: 0.7559 (t80) REVERT: C 178 PHE cc_start: 0.9069 (m-10) cc_final: 0.8611 (m-10) REVERT: C 179 TYR cc_start: 0.7817 (t80) cc_final: 0.7518 (t80) REVERT: C 231 LEU cc_start: 0.9192 (mt) cc_final: 0.8950 (mt) REVERT: C 274 ASP cc_start: 0.8378 (p0) cc_final: 0.7992 (p0) REVERT: D 25 ASN cc_start: 0.9394 (m-40) cc_final: 0.8999 (m-40) REVERT: D 29 PHE cc_start: 0.7425 (p90) cc_final: 0.7172 (p90) REVERT: E 24 PHE cc_start: 0.9215 (m-10) cc_final: 0.8820 (m-80) REVERT: E 25 TRP cc_start: 0.8219 (p-90) cc_final: 0.7857 (p-90) REVERT: E 46 MET cc_start: 0.8224 (tpp) cc_final: 0.7886 (tpp) REVERT: E 67 TYR cc_start: 0.8800 (m-80) cc_final: 0.8414 (m-80) REVERT: E 70 MET cc_start: 0.7997 (mpp) cc_final: 0.7295 (mpp) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.1251 time to fit residues: 125.0371 Evaluate side-chains 548 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098760 restraints weight = 42383.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102053 restraints weight = 22762.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104193 restraints weight = 14448.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105713 restraints weight = 10324.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106647 restraints weight = 8078.450| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17041 Z= 0.139 Angle : 0.666 12.971 23026 Z= 0.349 Chirality : 0.045 0.202 2464 Planarity : 0.004 0.050 2931 Dihedral : 7.877 138.790 2373 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2012 helix: 0.90 (0.15), residues: 1139 sheet: 0.64 (0.46), residues: 127 loop : -0.22 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.025 0.002 TYR C 173 PHE 0.040 0.002 PHE A 234 TRP 0.010 0.001 TRP B 9 HIS 0.009 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17038) covalent geometry : angle 0.66140 / 0.35 (23020) SS BOND : bond 0.00683 / 0.34 ( 3) SS BOND : angle 4.69070 / 2.28 ( 6) hydrogen bonds : bond 0.03830 / 2.49 ( 912) hydrogen bonds : angle 5.06165 / 3.56 ( 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 658 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.682 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 113 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9125 (mmmm) REVERT: A 147 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8377 (tp-100) REVERT: A 150 GLN cc_start: 0.8668 (tp40) cc_final: 0.8414 (tp40) REVERT: A 158 ASN cc_start: 0.9152 (m-40) cc_final: 0.8918 (m110) REVERT: A 184 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.9152 (mmm160) REVERT: A 227 MET cc_start: 0.9270 (ptp) cc_final: 0.9063 (ptp) REVERT: A 228 LYS cc_start: 0.9031 (tptt) cc_final: 0.8546 (tptt) REVERT: A 250 TYR cc_start: 0.8183 (m-80) cc_final: 0.7892 (m-80) REVERT: A 290 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8462 (tm-30) REVERT: A 291 LEU cc_start: 0.9468 (mm) cc_final: 0.8922 (mm) REVERT: A 301 PHE cc_start: 0.8992 (m-80) cc_final: 0.8622 (m-80) REVERT: A 358 ILE cc_start: 0.9033 (mm) cc_final: 0.8807 (mm) REVERT: A 390 GLN cc_start: 0.8809 (mt0) cc_final: 0.8546 (mt0) REVERT: A 418 ASN cc_start: 0.8966 (m-40) cc_final: 0.8550 (m110) REVERT: A 446 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.8005 (tpp-160) REVERT: A 456 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8965 (mtmm) REVERT: A 471 TYR cc_start: 0.8513 (t80) cc_final: 0.8061 (t80) REVERT: A 474 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 515 ASP cc_start: 0.8832 (m-30) cc_final: 0.8397 (m-30) REVERT: A 570 MET cc_start: 0.8291 (ptm) cc_final: 0.7958 (ptt) REVERT: A 615 MET cc_start: 0.8895 (mmm) cc_final: 0.8475 (mmm) REVERT: A 645 GLN cc_start: 0.8696 (tp40) cc_final: 0.8243 (tp-100) REVERT: A 661 THR cc_start: 0.9612 (p) cc_final: 0.9145 (p) REVERT: B 9 TRP cc_start: 0.9459 (p90) cc_final: 0.8944 (p90) REVERT: B 30 LYS cc_start: 0.9330 (tmtt) cc_final: 0.9107 (tptt) REVERT: B 64 TYR cc_start: 0.8625 (m-10) cc_final: 0.8275 (m-10) REVERT: B 87 LYS cc_start: 0.9020 (tppt) cc_final: 0.8501 (tptp) REVERT: B 109 ASN cc_start: 0.8963 (m-40) cc_final: 0.8642 (p0) REVERT: B 127 LEU cc_start: 0.9767 (mt) cc_final: 0.9476 (mm) REVERT: B 129 PHE cc_start: 0.9142 (m-10) cc_final: 0.8817 (m-80) REVERT: B 138 LYS cc_start: 0.9412 (mtpt) cc_final: 0.9073 (mttt) REVERT: B 147 GLN cc_start: 0.8964 (mt0) cc_final: 0.8353 (mt0) REVERT: B 184 ARG cc_start: 0.9519 (tpp80) cc_final: 0.9109 (tpp80) REVERT: B 186 ILE cc_start: 0.9530 (mt) cc_final: 0.9314 (mt) REVERT: B 190 MET cc_start: 0.9397 (mtm) cc_final: 0.8976 (mtm) REVERT: B 223 VAL cc_start: 0.9584 (m) cc_final: 0.9339 (p) REVERT: B 231 ASP cc_start: 0.8710 (t70) cc_final: 0.7559 (t70) REVERT: B 232 ASN cc_start: 0.9052 (m-40) cc_final: 0.8665 (m110) REVERT: B 235 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8002 (mtm-85) REVERT: B 240 MET cc_start: 0.7768 (ppp) cc_final: 0.7198 (ppp) REVERT: B 258 ILE cc_start: 0.9425 (tp) cc_final: 0.9121 (tp) REVERT: B 286 ASP cc_start: 0.8652 (m-30) cc_final: 0.8090 (m-30) REVERT: B 316 GLU cc_start: 0.9302 (tt0) cc_final: 0.9083 (tt0) REVERT: B 335 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 348 MET cc_start: 0.8994 (ppp) cc_final: 0.8438 (ppp) REVERT: B 349 LEU cc_start: 0.9289 (mt) cc_final: 0.8575 (mt) REVERT: B 370 ASN cc_start: 0.9531 (m-40) cc_final: 0.9086 (m110) REVERT: B 378 PHE cc_start: 0.8918 (p90) cc_final: 0.8562 (p90) REVERT: B 402 GLU cc_start: 0.8366 (mp0) cc_final: 0.7786 (mp0) REVERT: B 425 ILE cc_start: 0.9042 (mt) cc_final: 0.8791 (mt) REVERT: B 427 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8554 (ptmt) REVERT: B 437 THR cc_start: 0.9466 (m) cc_final: 0.9148 (m) REVERT: B 489 ASN cc_start: 0.9081 (t0) cc_final: 0.8756 (t0) REVERT: B 490 THR cc_start: 0.9397 (m) cc_final: 0.9153 (p) REVERT: B 550 MET cc_start: 0.7816 (mtp) cc_final: 0.7400 (mtt) REVERT: B 574 TYR cc_start: 0.8488 (m-80) cc_final: 0.8038 (m-80) REVERT: B 623 TRP cc_start: 0.8790 (t-100) cc_final: 0.8172 (t-100) REVERT: B 656 LEU cc_start: 0.9248 (mt) cc_final: 0.9015 (mt) REVERT: C 17 PHE cc_start: 0.9048 (p90) cc_final: 0.8346 (p90) REVERT: C 20 MET cc_start: 0.9472 (ppp) cc_final: 0.9254 (ppp) REVERT: C 21 PHE cc_start: 0.9133 (m-80) cc_final: 0.8592 (m-80) REVERT: C 46 TYR cc_start: 0.7782 (m-80) cc_final: 0.7416 (m-80) REVERT: C 56 MET cc_start: 0.0334 (ptm) cc_final: -0.0317 (ttm) REVERT: C 68 GLU cc_start: 0.8879 (mp0) cc_final: 0.8494 (pm20) REVERT: C 74 MET cc_start: 0.9357 (mpp) cc_final: 0.9029 (mpp) REVERT: C 87 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8726 (ptpp) REVERT: C 89 VAL cc_start: 0.7591 (t) cc_final: 0.7123 (t) REVERT: C 95 MET cc_start: 0.8585 (ttp) cc_final: 0.7742 (ttp) REVERT: C 127 GLN cc_start: 0.9393 (pt0) cc_final: 0.9110 (pp30) REVERT: C 157 MET cc_start: 0.9415 (mtm) cc_final: 0.8866 (ptp) REVERT: C 174 TYR cc_start: 0.8925 (t80) cc_final: 0.7639 (t80) REVERT: C 178 PHE cc_start: 0.9088 (m-10) cc_final: 0.8584 (m-10) REVERT: C 231 LEU cc_start: 0.9207 (mt) cc_final: 0.8962 (mt) REVERT: C 274 ASP cc_start: 0.8395 (p0) cc_final: 0.8001 (p0) REVERT: D 25 ASN cc_start: 0.9364 (m-40) cc_final: 0.8879 (m-40) REVERT: D 29 PHE cc_start: 0.7477 (p90) cc_final: 0.7239 (p90) REVERT: D 92 PHE cc_start: 0.6662 (t80) cc_final: 0.5853 (t80) REVERT: E 24 PHE cc_start: 0.9237 (m-10) cc_final: 0.8879 (m-80) REVERT: E 25 TRP cc_start: 0.8323 (p-90) cc_final: 0.7616 (p-90) REVERT: E 46 MET cc_start: 0.8274 (tpp) cc_final: 0.7954 (tpp) REVERT: E 67 TYR cc_start: 0.8781 (m-80) cc_final: 0.8380 (m-80) REVERT: E 70 MET cc_start: 0.7700 (mpp) cc_final: 0.7058 (mpp) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.1306 time to fit residues: 131.9413 Evaluate side-chains 563 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 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** B 25 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099469 restraints weight = 42816.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102993 restraints weight = 22516.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105226 restraints weight = 14093.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106579 restraints weight = 10157.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107583 restraints weight = 8142.095| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17041 Z= 0.170 Angle : 0.675 12.239 23026 Z= 0.355 Chirality : 0.045 0.201 2464 Planarity : 0.004 0.057 2931 Dihedral : 7.894 141.048 2373 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.62 (0.19), residues: 2012 helix: 0.89 (0.15), residues: 1147 sheet: -0.08 (0.42), residues: 157 loop : -0.08 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.027 0.002 TYR C 173 PHE 0.034 0.002 PHE C 172 TRP 0.016 0.002 TRP A 623 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (17038) covalent geometry : angle 0.67051 / 0.35 (23020) SS BOND : bond 0.00647 / 0.32 ( 3) SS BOND : angle 4.86067 / 2.38 ( 6) hydrogen bonds : bond 0.03841 / 2.50 ( 912) hydrogen bonds : angle 5.07627 / 3.58 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.19 seconds wall clock time: 70 minutes 48.72 seconds (4248.72 seconds total)