Starting phenix.real_space_refine on Sun Aug 24 03:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxx_45014/08_2025/9bxx_45014.map" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10641 2.51 5 N 2712 2.21 5 O 3216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.55, per 1000 atoms: 0.21 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 139.932, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 87 16.00 P 16 15.00 Mg 2 11.99 O 3216 8.00 N 2712 7.00 C 10641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 734.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.260A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.788A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.232A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.568A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.634A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.880A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.513A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.255A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.233A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.022A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.818A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.468A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5044 1.34 - 1.46: 3105 1.46 - 1.58: 8700 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17038 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.40e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.59e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.91e+00 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22240 2.09 - 4.19: 705 4.19 - 6.28: 64 6.28 - 8.37: 9 8.37 - 10.46: 2 Bond angle restraints: 23020 Sorted by residual: angle pdb=" C VAL E 69 " pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " ideal model delta sigma weight residual 111.15 119.33 -8.18 1.30e+00 5.92e-01 3.96e+01 angle pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " pdb=" CG1 VAL E 69 " ideal model delta sigma weight residual 110.40 118.71 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.50 -4.31 1.06e+00 8.90e-01 1.65e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 9642 29.73 - 59.46: 547 59.46 - 89.19: 60 89.19 - 118.92: 3 118.92 - 148.65: 4 Dihedral angle restraints: 10256 sinusoidal: 4264 harmonic: 5992 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.28 84.28 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 153.03 148.65 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 156.37 145.31 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 10253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2223 0.093 - 0.186: 203 0.186 - 0.280: 33 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.078 2.00e-02 2.50e+03 3.70e-02 3.43e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.041 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP B 623 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 124 2.51 - 3.11: 12002 3.11 - 3.70: 27791 3.70 - 4.30: 42534 4.30 - 4.90: 68522 Nonbonded interactions: 150973 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.630 17041 Z= 0.416 Angle : 0.829 13.547 23026 Z= 0.517 Chirality : 0.059 0.466 2464 Planarity : 0.004 0.041 2931 Dihedral : 17.544 148.652 6399 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 16.27 % Favored : 82.34 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.31 (0.37), residues: 179 loop : 0.43 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.029 0.002 TYR E 67 PHE 0.021 0.002 PHE D 92 TRP 0.078 0.006 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00603 (17038) covalent geometry : angle 0.82349 (23020) SS BOND : bond 0.36353 ( 3) SS BOND : angle 6.09121 ( 6) hydrogen bonds : bond 0.16740 ( 912) hydrogen bonds : angle 6.70338 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 863 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8493 (mt) cc_final: 0.8243 (mm) REVERT: A 99 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8873 (mmmm) REVERT: A 147 GLN cc_start: 0.8226 (mt0) cc_final: 0.7777 (mt0) REVERT: A 181 ASP cc_start: 0.8683 (m-30) cc_final: 0.8333 (m-30) REVERT: A 188 ILE cc_start: 0.8849 (mt) cc_final: 0.8432 (mt) REVERT: A 213 ILE cc_start: 0.7163 (mt) cc_final: 0.6951 (tp) REVERT: A 216 VAL cc_start: 0.8023 (p) cc_final: 0.7802 (m) REVERT: A 257 ASP cc_start: 0.8033 (m-30) cc_final: 0.7790 (m-30) REVERT: A 466 MET cc_start: 0.6595 (ptt) cc_final: 0.6350 (ptt) REVERT: A 493 MET cc_start: 0.8059 (tmm) cc_final: 0.7835 (tmm) REVERT: A 500 ILE cc_start: 0.9119 (mt) cc_final: 0.8752 (mt) REVERT: A 501 GLN cc_start: 0.8436 (tt0) cc_final: 0.8065 (tt0) REVERT: A 506 ILE cc_start: 0.8783 (mt) cc_final: 0.8354 (mt) REVERT: A 553 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: A 594 VAL cc_start: 0.8429 (m) cc_final: 0.8164 (m) REVERT: A 630 TYR cc_start: 0.6513 (m-80) cc_final: 0.5058 (m-80) REVERT: A 644 ILE cc_start: 0.9047 (mt) cc_final: 0.8674 (mt) REVERT: B 68 PHE cc_start: 0.8403 (p90) cc_final: 0.7992 (p90) REVERT: B 69 LEU cc_start: 0.8205 (mt) cc_final: 0.7921 (mt) REVERT: B 87 LYS cc_start: 0.8400 (tptp) cc_final: 0.8112 (tptp) REVERT: B 172 LEU cc_start: 0.8956 (mp) cc_final: 0.8645 (mp) REVERT: B 175 VAL cc_start: 0.9060 (t) cc_final: 0.8839 (t) REVERT: B 204 SER cc_start: 0.8686 (m) cc_final: 0.7745 (t) REVERT: B 257 ASP cc_start: 0.8565 (m-30) cc_final: 0.7957 (m-30) REVERT: B 258 ILE cc_start: 0.8603 (tp) cc_final: 0.8400 (tp) REVERT: B 277 THR cc_start: 0.7976 (p) cc_final: 0.7406 (p) REVERT: B 322 MET cc_start: 0.7121 (mmm) cc_final: 0.6280 (mmm) REVERT: B 349 LEU cc_start: 0.8910 (mt) cc_final: 0.8697 (mt) REVERT: B 391 VAL cc_start: 0.9041 (p) cc_final: 0.8766 (p) REVERT: B 468 LEU cc_start: 0.8582 (tp) cc_final: 0.8342 (tp) REVERT: B 472 LEU cc_start: 0.8818 (mt) cc_final: 0.8457 (mt) REVERT: B 493 MET cc_start: 0.7793 (tmm) cc_final: 0.7573 (tmm) REVERT: B 550 MET cc_start: 0.7183 (mtm) cc_final: 0.6876 (mtp) REVERT: B 565 VAL cc_start: 0.9021 (t) cc_final: 0.8609 (m) REVERT: B 574 TYR cc_start: 0.7844 (m-80) cc_final: 0.7504 (m-80) REVERT: B 575 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7342 (mtm-85) REVERT: B 576 LEU cc_start: 0.8791 (mt) cc_final: 0.8411 (mt) REVERT: B 589 SER cc_start: 0.8776 (m) cc_final: 0.8316 (m) REVERT: B 645 GLN cc_start: 0.8022 (tp40) cc_final: 0.7686 (tp40) REVERT: B 658 LEU cc_start: 0.8882 (mt) cc_final: 0.8638 (mp) REVERT: B 664 THR cc_start: 0.8929 (p) cc_final: 0.8567 (t) REVERT: C 33 GLU cc_start: 0.1904 (mp0) cc_final: 0.1276 (tm-30) REVERT: C 153 LEU cc_start: 0.6439 (tp) cc_final: 0.6109 (tp) REVERT: C 201 HIS cc_start: 0.3596 (m170) cc_final: 0.2464 (m170) REVERT: C 316 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6705 (mtmm) REVERT: D 63 THR cc_start: 0.5201 (m) cc_final: 0.4949 (m) REVERT: D 286 VAL cc_start: 0.3482 (t) cc_final: 0.2961 (p) REVERT: E 78 LEU cc_start: 0.6809 (mp) cc_final: 0.6305 (mp) outliers start: 25 outliers final: 3 residues processed: 874 average time/residue: 0.1315 time to fit residues: 167.9456 Evaluate side-chains 577 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 573 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 232 ASN A 320 ASN A 370 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 61 ASN B 304 HIS B 447 ASN C 24 GLN C 28 GLN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106230 restraints weight = 43782.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110313 restraints weight = 26743.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113025 restraints weight = 18038.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114900 restraints weight = 13505.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116225 restraints weight = 10837.660| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17041 Z= 0.259 Angle : 0.730 14.704 23026 Z= 0.384 Chirality : 0.046 0.241 2464 Planarity : 0.005 0.055 2931 Dihedral : 10.913 162.812 2325 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.34 % Allowed : 3.63 % Favored : 96.03 % 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 aren not related in a simple way. whole: 1.02 (0.18), residues: 2012 helix: 1.14 (0.15), residues: 1160 sheet: -0.39 (0.35), residues: 177 loop : 0.40 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.036 0.002 TYR B 36 PHE 0.027 0.003 PHE A 492 TRP 0.023 0.002 TRP B 558 HIS 0.009 0.002 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00540 (17038) covalent geometry : angle 0.71897 (23020) SS BOND : bond 0.03074 ( 3) SS BOND : angle 7.69979 ( 6) hydrogen bonds : bond 0.05050 ( 912) hydrogen bonds : angle 5.28420 ( 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 653 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 647 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.9373 (m-80) cc_final: 0.9073 (m-80) REVERT: A 99 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9326 (tppp) REVERT: A 147 GLN cc_start: 0.9136 (mt0) cc_final: 0.8577 (mt0) REVERT: A 186 ILE cc_start: 0.9548 (mm) cc_final: 0.9254 (mm) REVERT: A 190 MET cc_start: 0.9284 (mtm) cc_final: 0.8956 (mtm) REVERT: A 250 TYR cc_start: 0.7237 (m-80) cc_final: 0.6873 (m-80) REVERT: A 257 ASP cc_start: 0.8670 (m-30) cc_final: 0.8052 (m-30) REVERT: A 262 LEU cc_start: 0.9640 (mt) cc_final: 0.9418 (mt) REVERT: A 263 ASP cc_start: 0.8957 (m-30) cc_final: 0.8577 (m-30) REVERT: A 301 PHE cc_start: 0.8931 (m-80) cc_final: 0.8132 (m-10) REVERT: A 312 GLN cc_start: 0.8785 (tp40) cc_final: 0.8576 (tp40) REVERT: A 362 ASP cc_start: 0.8419 (m-30) cc_final: 0.8001 (m-30) REVERT: A 367 VAL cc_start: 0.9616 (m) cc_final: 0.9379 (p) REVERT: A 466 MET cc_start: 0.9038 (ptt) cc_final: 0.8724 (ptt) REVERT: A 475 ASN cc_start: 0.8879 (m-40) cc_final: 0.8564 (m110) REVERT: A 501 GLN cc_start: 0.9438 (tt0) cc_final: 0.8988 (tm-30) REVERT: A 516 GLN cc_start: 0.9254 (tt0) cc_final: 0.8839 (tt0) REVERT: A 571 TYR cc_start: 0.8645 (t80) cc_final: 0.8026 (t80) REVERT: A 586 TYR cc_start: 0.8944 (m-80) cc_final: 0.8733 (m-80) REVERT: A 628 GLU cc_start: 0.9244 (tt0) cc_final: 0.8954 (tt0) REVERT: A 632 MET cc_start: 0.8289 (mtt) cc_final: 0.8030 (mtm) REVERT: A 645 GLN cc_start: 0.8603 (tp40) cc_final: 0.8119 (tp40) REVERT: A 650 GLN cc_start: 0.8343 (mt0) cc_final: 0.7416 (mt0) REVERT: A 664 THR cc_start: 0.9344 (p) cc_final: 0.8842 (p) REVERT: A 668 ASN cc_start: 0.9039 (m-40) cc_final: 0.8415 (m-40) REVERT: A 686 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7368 (tpt90) REVERT: B 23 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9020 (mmmt) REVERT: B 128 PHE cc_start: 0.9666 (t80) cc_final: 0.9455 (t80) REVERT: B 139 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8847 (mt-10) REVERT: B 144 MET cc_start: 0.9336 (mtm) cc_final: 0.8527 (mtm) REVERT: B 145 ILE cc_start: 0.9433 (tp) cc_final: 0.8963 (tp) REVERT: B 147 GLN cc_start: 0.9397 (mt0) cc_final: 0.9175 (mp10) REVERT: B 172 LEU cc_start: 0.8815 (mp) cc_final: 0.8538 (mp) REVERT: B 184 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8336 (ttm170) REVERT: B 186 ILE cc_start: 0.9713 (mt) cc_final: 0.9464 (mt) REVERT: B 190 MET cc_start: 0.9426 (mtm) cc_final: 0.8910 (mtm) REVERT: B 239 GLN cc_start: 0.7654 (mt0) cc_final: 0.7060 (mm-40) REVERT: B 250 TYR cc_start: 0.8321 (m-80) cc_final: 0.7965 (m-80) REVERT: B 335 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 348 MET cc_start: 0.8540 (tpt) cc_final: 0.8240 (tpp) REVERT: B 375 LYS cc_start: 0.8411 (mmmm) cc_final: 0.8137 (mmmm) REVERT: B 377 LYS cc_start: 0.7767 (mttt) cc_final: 0.7518 (mttt) REVERT: B 403 ILE cc_start: 0.9266 (mm) cc_final: 0.9026 (mm) REVERT: B 416 ILE cc_start: 0.9114 (mm) cc_final: 0.8800 (mm) REVERT: B 420 MET cc_start: 0.9019 (mmm) cc_final: 0.8707 (mmp) REVERT: B 425 ILE cc_start: 0.9358 (mt) cc_final: 0.9123 (mt) REVERT: B 496 ASN cc_start: 0.9406 (t0) cc_final: 0.9060 (t0) REVERT: B 501 GLN cc_start: 0.9536 (tt0) cc_final: 0.9243 (tt0) REVERT: B 576 LEU cc_start: 0.9235 (mt) cc_final: 0.9005 (mt) REVERT: B 604 ARG cc_start: 0.9302 (mmp80) cc_final: 0.8906 (mmp80) REVERT: B 640 MET cc_start: 0.9134 (tpp) cc_final: 0.8881 (tpp) REVERT: B 645 GLN cc_start: 0.9209 (tp40) cc_final: 0.8936 (tp-100) REVERT: B 650 GLN cc_start: 0.6691 (mt0) cc_final: 0.5944 (mt0) REVERT: B 686 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8013 (mmm160) REVERT: C 33 GLU cc_start: 0.4562 (mp0) cc_final: 0.4211 (pp20) REVERT: C 157 MET cc_start: 0.8646 (mtm) cc_final: 0.8212 (mtm) REVERT: C 162 TYR cc_start: 0.7771 (m-80) cc_final: 0.7474 (m-10) REVERT: C 177 TYR cc_start: 0.8958 (t80) cc_final: 0.8628 (t80) REVERT: C 198 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5425 (mt-10) REVERT: D 82 ASP cc_start: 0.8838 (m-30) cc_final: 0.8438 (p0) REVERT: D 137 MET cc_start: 0.5884 (ttt) cc_final: 0.5331 (tmm) REVERT: D 179 TYR cc_start: 0.8182 (t80) cc_final: 0.7878 (t80) REVERT: D 185 MET cc_start: 0.4333 (mmp) cc_final: 0.3993 (mpp) REVERT: D 242 TYR cc_start: 0.9013 (t80) cc_final: 0.8563 (t80) REVERT: D 262 TYR cc_start: 0.8620 (t80) cc_final: 0.8335 (t80) REVERT: E 25 TRP cc_start: 0.7769 (p-90) cc_final: 0.6785 (p-90) outliers start: 6 outliers final: 1 residues processed: 649 average time/residue: 0.1276 time to fit residues: 124.6721 Evaluate side-chains 529 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 467 ASN A 568 HIS B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS B 447 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.152901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106734 restraints weight = 44803.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110806 restraints weight = 27640.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113533 restraints weight = 18886.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115411 restraints weight = 14102.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116737 restraints weight = 11256.845| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17041 Z= 0.163 Angle : 0.631 8.723 23026 Z= 0.330 Chirality : 0.043 0.226 2464 Planarity : 0.004 0.039 2931 Dihedral : 10.710 162.643 2325 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.17 % Allowed : 2.52 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.18), residues: 2012 helix: 1.22 (0.15), residues: 1154 sheet: 0.37 (0.43), residues: 141 loop : 0.22 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.028 0.002 TYR B 36 PHE 0.040 0.002 PHE C 92 TRP 0.010 0.001 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00353 (17038) covalent geometry : angle 0.62802 (23020) SS BOND : bond 0.02021 ( 3) SS BOND : angle 3.81004 ( 6) hydrogen bonds : bond 0.04435 ( 912) hydrogen bonds : angle 5.03616 ( 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 632 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 629 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8834 (m) cc_final: 0.8578 (t) REVERT: A 142 ASN cc_start: 0.9272 (m-40) cc_final: 0.8999 (m110) REVERT: A 147 GLN cc_start: 0.9196 (mt0) cc_final: 0.7805 (mt0) REVERT: A 186 ILE cc_start: 0.9543 (mm) cc_final: 0.9188 (mm) REVERT: A 190 MET cc_start: 0.9323 (mtm) cc_final: 0.9001 (mtm) REVERT: A 213 ILE cc_start: 0.9121 (mt) cc_final: 0.8904 (tp) REVERT: A 250 TYR cc_start: 0.7249 (m-80) cc_final: 0.6798 (m-80) REVERT: A 257 ASP cc_start: 0.8690 (m-30) cc_final: 0.8278 (m-30) REVERT: A 263 ASP cc_start: 0.9051 (m-30) cc_final: 0.8673 (m-30) REVERT: A 291 LEU cc_start: 0.9683 (mp) cc_final: 0.9357 (mp) REVERT: A 301 PHE cc_start: 0.8893 (m-80) cc_final: 0.8356 (m-80) REVERT: A 312 GLN cc_start: 0.8603 (tp40) cc_final: 0.8252 (tp40) REVERT: A 317 MET cc_start: 0.9054 (mmm) cc_final: 0.8816 (mmm) REVERT: A 322 MET cc_start: 0.8944 (mmm) cc_final: 0.8689 (mmm) REVERT: A 352 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 362 ASP cc_start: 0.8373 (m-30) cc_final: 0.7902 (m-30) REVERT: A 366 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8816 (ptpp) REVERT: A 475 ASN cc_start: 0.8790 (m-40) cc_final: 0.8392 (m110) REVERT: A 501 GLN cc_start: 0.9428 (tt0) cc_final: 0.9037 (tm-30) REVERT: A 509 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8922 (tm-30) REVERT: A 571 TYR cc_start: 0.8774 (t80) cc_final: 0.8505 (t80) REVERT: A 588 GLN cc_start: 0.8975 (mm-40) cc_final: 0.7959 (mm-40) REVERT: A 598 MET cc_start: 0.8410 (mtp) cc_final: 0.8151 (mtp) REVERT: A 604 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8527 (tpp80) REVERT: A 628 GLU cc_start: 0.9270 (tt0) cc_final: 0.8853 (tt0) REVERT: A 645 GLN cc_start: 0.8582 (tp40) cc_final: 0.8176 (tp40) REVERT: A 650 GLN cc_start: 0.8383 (mt0) cc_final: 0.7458 (mt0) REVERT: A 664 THR cc_start: 0.9378 (p) cc_final: 0.8863 (p) REVERT: A 668 ASN cc_start: 0.8906 (m-40) cc_final: 0.8483 (m-40) REVERT: A 686 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7300 (mmm160) REVERT: B 10 ILE cc_start: 0.9723 (mt) cc_final: 0.9430 (tp) REVERT: B 23 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9070 (mmtm) REVERT: B 99 LYS cc_start: 0.9352 (tptm) cc_final: 0.9011 (tptm) REVERT: B 100 PHE cc_start: 0.9448 (t80) cc_final: 0.9232 (t80) REVERT: B 139 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8862 (mt-10) REVERT: B 144 MET cc_start: 0.9167 (mtm) cc_final: 0.8927 (mtm) REVERT: B 172 LEU cc_start: 0.8791 (mp) cc_final: 0.8505 (mp) REVERT: B 184 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8615 (ttm-80) REVERT: B 186 ILE cc_start: 0.9733 (mt) cc_final: 0.9471 (mt) REVERT: B 190 MET cc_start: 0.9423 (mtm) cc_final: 0.9158 (mtm) REVERT: B 317 MET cc_start: 0.8641 (mtt) cc_final: 0.8396 (mpp) REVERT: B 335 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 349 LEU cc_start: 0.9599 (mt) cc_final: 0.9381 (mt) REVERT: B 350 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8660 (mtp-110) REVERT: B 375 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8164 (mtpt) REVERT: B 403 ILE cc_start: 0.9200 (mm) cc_final: 0.8917 (mm) REVERT: B 496 ASN cc_start: 0.9389 (t0) cc_final: 0.8842 (t0) REVERT: B 501 GLN cc_start: 0.9551 (tt0) cc_final: 0.9314 (tt0) REVERT: B 576 LEU cc_start: 0.9294 (mt) cc_final: 0.9042 (mt) REVERT: B 636 LYS cc_start: 0.9446 (mmpt) cc_final: 0.9140 (mmmt) REVERT: B 640 MET cc_start: 0.9152 (tpp) cc_final: 0.8876 (tpp) REVERT: B 645 GLN cc_start: 0.9144 (tp40) cc_final: 0.8840 (tp-100) REVERT: B 650 GLN cc_start: 0.6807 (mt0) cc_final: 0.6033 (mt0) REVERT: B 664 THR cc_start: 0.8862 (p) cc_final: 0.8569 (t) REVERT: C 33 GLU cc_start: 0.4312 (mp0) cc_final: 0.4012 (pp20) REVERT: C 157 MET cc_start: 0.8350 (mtm) cc_final: 0.7639 (mtm) REVERT: D 82 ASP cc_start: 0.8890 (m-30) cc_final: 0.8196 (p0) REVERT: D 137 MET cc_start: 0.6031 (ttt) cc_final: 0.5691 (tmm) REVERT: D 227 PHE cc_start: 0.7097 (t80) cc_final: 0.6713 (t80) REVERT: D 262 TYR cc_start: 0.8669 (t80) cc_final: 0.8399 (t80) REVERT: E 25 TRP cc_start: 0.7816 (p-90) cc_final: 0.6614 (p-90) outliers start: 3 outliers final: 1 residues processed: 630 average time/residue: 0.1235 time to fit residues: 116.9617 Evaluate side-chains 524 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 180 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104789 restraints weight = 44461.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108831 restraints weight = 27501.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111562 restraints weight = 18689.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112658 restraints weight = 14072.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114420 restraints weight = 11774.048| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17041 Z= 0.141 Angle : 0.612 9.778 23026 Z= 0.319 Chirality : 0.043 0.190 2464 Planarity : 0.004 0.045 2931 Dihedral : 10.451 158.393 2325 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2012 helix: 1.23 (0.15), residues: 1164 sheet: -0.38 (0.38), residues: 183 loop : 0.23 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 575 TYR 0.022 0.002 TYR B 36 PHE 0.027 0.002 PHE A 492 TRP 0.006 0.001 TRP B 558 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00310 (17038) covalent geometry : angle 0.60809 (23020) SS BOND : bond 0.00391 ( 3) SS BOND : angle 4.56893 ( 6) hydrogen bonds : bond 0.04120 ( 912) hydrogen bonds : angle 4.92671 ( 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 620 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 0.601 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: symmetry clash REVERT: A 37 PHE cc_start: 0.9087 (m-80) cc_final: 0.8876 (m-80) REVERT: A 65 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7401 (mp0) REVERT: A 186 ILE cc_start: 0.9547 (mm) cc_final: 0.9218 (mm) REVERT: A 188 ILE cc_start: 0.9569 (mt) cc_final: 0.9225 (mt) REVERT: A 190 MET cc_start: 0.9315 (mtm) cc_final: 0.9042 (mtm) REVERT: A 250 TYR cc_start: 0.7228 (m-80) cc_final: 0.6777 (m-80) REVERT: A 257 ASP cc_start: 0.8694 (m-30) cc_final: 0.8383 (m-30) REVERT: A 263 ASP cc_start: 0.9079 (m-30) cc_final: 0.8709 (m-30) REVERT: A 290 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 291 LEU cc_start: 0.9664 (mp) cc_final: 0.9198 (mt) REVERT: A 301 PHE cc_start: 0.8814 (m-80) cc_final: 0.8381 (m-80) REVERT: A 312 GLN cc_start: 0.8591 (tp40) cc_final: 0.8251 (tp40) REVERT: A 317 MET cc_start: 0.9097 (mmm) cc_final: 0.8759 (mmm) REVERT: A 322 MET cc_start: 0.8844 (mmm) cc_final: 0.8582 (mmm) REVERT: A 350 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7971 (mtp85) REVERT: A 494 MET cc_start: 0.8536 (mmt) cc_final: 0.8233 (mmt) REVERT: A 501 GLN cc_start: 0.9421 (tt0) cc_final: 0.8935 (tm-30) REVERT: A 571 TYR cc_start: 0.8772 (t80) cc_final: 0.8541 (t80) REVERT: A 586 TYR cc_start: 0.9117 (m-80) cc_final: 0.8436 (m-80) REVERT: A 615 MET cc_start: 0.8827 (mmp) cc_final: 0.8610 (mmp) REVERT: A 628 GLU cc_start: 0.9270 (tt0) cc_final: 0.8888 (tt0) REVERT: A 645 GLN cc_start: 0.8599 (tp40) cc_final: 0.8390 (tp40) REVERT: A 664 THR cc_start: 0.9394 (p) cc_final: 0.8897 (p) REVERT: A 667 LEU cc_start: 0.9301 (tt) cc_final: 0.9084 (tt) REVERT: A 668 ASN cc_start: 0.8869 (m-40) cc_final: 0.8525 (m-40) REVERT: A 686 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7441 (mmm160) REVERT: B 10 ILE cc_start: 0.9703 (mt) cc_final: 0.9397 (tp) REVERT: B 23 LYS cc_start: 0.9333 (mmtm) cc_final: 0.8941 (mmmt) REVERT: B 95 MET cc_start: 0.8818 (tpp) cc_final: 0.8561 (tpp) REVERT: B 99 LYS cc_start: 0.9463 (tptm) cc_final: 0.8967 (tptm) REVERT: B 100 PHE cc_start: 0.9416 (t80) cc_final: 0.9192 (t80) REVERT: B 129 PHE cc_start: 0.9432 (m-80) cc_final: 0.9127 (m-80) REVERT: B 144 MET cc_start: 0.9152 (mtm) cc_final: 0.8893 (mtm) REVERT: B 145 ILE cc_start: 0.9517 (tp) cc_final: 0.9314 (tp) REVERT: B 172 LEU cc_start: 0.8820 (mp) cc_final: 0.8607 (mp) REVERT: B 184 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8455 (ttm-80) REVERT: B 186 ILE cc_start: 0.9647 (mt) cc_final: 0.9425 (mt) REVERT: B 190 MET cc_start: 0.9421 (mtm) cc_final: 0.9108 (mtm) REVERT: B 235 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8265 (mtm-85) REVERT: B 317 MET cc_start: 0.8594 (mtt) cc_final: 0.8323 (mpp) REVERT: B 319 MET cc_start: 0.8572 (tpp) cc_final: 0.8228 (tpp) REVERT: B 335 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 348 MET cc_start: 0.8416 (tpt) cc_final: 0.8204 (tpp) REVERT: B 349 LEU cc_start: 0.9575 (mt) cc_final: 0.9351 (mt) REVERT: B 403 ILE cc_start: 0.9213 (mm) cc_final: 0.8961 (mm) REVERT: B 475 ASN cc_start: 0.9228 (m-40) cc_final: 0.8803 (m-40) REVERT: B 496 ASN cc_start: 0.9424 (t0) cc_final: 0.9033 (t0) REVERT: B 598 MET cc_start: 0.8751 (ttp) cc_final: 0.8541 (ttp) REVERT: B 604 ARG cc_start: 0.9236 (mmp80) cc_final: 0.9004 (mmp80) REVERT: B 640 MET cc_start: 0.9028 (tpp) cc_final: 0.8764 (tpp) REVERT: B 645 GLN cc_start: 0.9223 (tp40) cc_final: 0.8788 (tp40) REVERT: B 650 GLN cc_start: 0.6799 (mt0) cc_final: 0.6575 (mt0) REVERT: C 157 MET cc_start: 0.8221 (mtm) cc_final: 0.7735 (mtm) REVERT: C 200 ILE cc_start: 0.8570 (pt) cc_final: 0.8339 (pt) REVERT: C 276 TYR cc_start: 0.8266 (t80) cc_final: 0.8005 (t80) REVERT: D 82 ASP cc_start: 0.8914 (m-30) cc_final: 0.8307 (p0) REVERT: D 137 MET cc_start: 0.6443 (ttt) cc_final: 0.6067 (tmm) REVERT: D 235 LEU cc_start: 0.7909 (mp) cc_final: 0.7655 (mt) REVERT: D 242 TYR cc_start: 0.9132 (t80) cc_final: 0.8754 (t80) REVERT: D 262 TYR cc_start: 0.8678 (t80) cc_final: 0.8429 (t80) REVERT: E 25 TRP cc_start: 0.7845 (p-90) cc_final: 0.6632 (p-90) REVERT: E 34 MET cc_start: 0.9021 (mpp) cc_final: 0.8794 (ptp) outliers start: 2 outliers final: 2 residues processed: 620 average time/residue: 0.1340 time to fit residues: 124.5290 Evaluate side-chains 527 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 525 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 19 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102058 restraints weight = 45594.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105985 restraints weight = 27730.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108652 restraints weight = 18730.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110429 restraints weight = 13978.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111680 restraints weight = 11204.992| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17041 Z= 0.203 Angle : 0.650 9.021 23026 Z= 0.341 Chirality : 0.044 0.191 2464 Planarity : 0.004 0.045 2931 Dihedral : 10.195 156.317 2325 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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 aren not related in a simple way. whole: 0.85 (0.18), residues: 2012 helix: 1.09 (0.15), residues: 1168 sheet: -0.44 (0.37), residues: 189 loop : 0.14 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 161 TYR 0.021 0.002 TYR D 105 PHE 0.029 0.002 PHE A 654 TRP 0.011 0.001 TRP A 623 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00434 (17038) covalent geometry : angle 0.64753 (23020) SS BOND : bond 0.00952 ( 3) SS BOND : angle 3.62991 ( 6) hydrogen bonds : bond 0.04111 ( 912) hydrogen bonds : angle 4.99424 ( 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 597 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 147 GLN cc_start: 0.8960 (mt0) cc_final: 0.8362 (mt0) REVERT: A 186 ILE cc_start: 0.9553 (mm) cc_final: 0.9191 (mm) REVERT: A 188 ILE cc_start: 0.9567 (mt) cc_final: 0.9306 (mt) REVERT: A 190 MET cc_start: 0.9296 (mtm) cc_final: 0.9071 (mtm) REVERT: A 250 TYR cc_start: 0.7296 (m-80) cc_final: 0.6922 (m-80) REVERT: A 255 HIS cc_start: 0.8237 (t-90) cc_final: 0.7707 (t70) REVERT: A 257 ASP cc_start: 0.8595 (m-30) cc_final: 0.8294 (m-30) REVERT: A 263 ASP cc_start: 0.9024 (m-30) cc_final: 0.8688 (m-30) REVERT: A 291 LEU cc_start: 0.9650 (mp) cc_final: 0.9209 (mt) REVERT: A 301 PHE cc_start: 0.8824 (m-80) cc_final: 0.8456 (m-80) REVERT: A 312 GLN cc_start: 0.8849 (tp40) cc_final: 0.8568 (tp40) REVERT: A 317 MET cc_start: 0.9097 (mmm) cc_final: 0.8822 (mmm) REVERT: A 322 MET cc_start: 0.8875 (mmm) cc_final: 0.8614 (mmm) REVERT: A 362 ASP cc_start: 0.8351 (m-30) cc_final: 0.7990 (m-30) REVERT: A 367 VAL cc_start: 0.9600 (m) cc_final: 0.9372 (p) REVERT: A 393 SER cc_start: 0.9177 (t) cc_final: 0.8256 (t) REVERT: A 402 GLU cc_start: 0.8212 (mp0) cc_final: 0.7534 (mp0) REVERT: A 447 ASN cc_start: 0.8863 (m-40) cc_final: 0.8563 (m-40) REVERT: A 501 GLN cc_start: 0.9445 (tt0) cc_final: 0.9019 (tm-30) REVERT: A 510 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8617 (tptp) REVERT: A 571 TYR cc_start: 0.8826 (t80) cc_final: 0.8070 (t80) REVERT: A 601 ILE cc_start: 0.9429 (tt) cc_final: 0.9059 (tt) REVERT: A 664 THR cc_start: 0.9375 (p) cc_final: 0.8948 (p) REVERT: A 668 ASN cc_start: 0.9077 (m-40) cc_final: 0.8845 (m-40) REVERT: A 686 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7745 (mmm160) REVERT: B 99 LYS cc_start: 0.9429 (tptm) cc_final: 0.9097 (tptp) REVERT: B 129 PHE cc_start: 0.9479 (m-80) cc_final: 0.9090 (m-80) REVERT: B 184 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8386 (ttm-80) REVERT: B 190 MET cc_start: 0.9378 (mtm) cc_final: 0.9116 (mtm) REVERT: B 205 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7629 (mmtm) REVERT: B 227 MET cc_start: 0.9264 (ptp) cc_final: 0.8600 (ptp) REVERT: B 235 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8103 (mtm-85) REVERT: B 274 ARG cc_start: 0.8423 (mmm160) cc_final: 0.7813 (mmm160) REVERT: B 317 MET cc_start: 0.8531 (mtt) cc_final: 0.8255 (mpp) REVERT: B 335 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 375 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8088 (mmmm) REVERT: B 403 ILE cc_start: 0.9156 (mm) cc_final: 0.8907 (mm) REVERT: B 471 TYR cc_start: 0.9225 (t80) cc_final: 0.8912 (t80) REVERT: B 475 ASN cc_start: 0.9118 (m-40) cc_final: 0.8761 (m-40) REVERT: B 496 ASN cc_start: 0.9469 (t0) cc_final: 0.9165 (t0) REVERT: B 546 LEU cc_start: 0.9250 (mt) cc_final: 0.8986 (mt) REVERT: B 576 LEU cc_start: 0.9294 (mt) cc_final: 0.9071 (mt) REVERT: B 586 TYR cc_start: 0.9523 (m-80) cc_final: 0.9176 (m-80) REVERT: B 645 GLN cc_start: 0.9199 (tp40) cc_final: 0.8772 (tp40) REVERT: B 650 GLN cc_start: 0.6570 (mt0) cc_final: 0.5872 (mt0) REVERT: B 652 ILE cc_start: 0.9359 (mt) cc_final: 0.9093 (mt) REVERT: C 157 MET cc_start: 0.8400 (mtm) cc_final: 0.8009 (mtm) REVERT: C 197 ASP cc_start: 0.7893 (m-30) cc_final: 0.6225 (m-30) REVERT: C 200 ILE cc_start: 0.8531 (pt) cc_final: 0.8203 (pt) REVERT: C 201 HIS cc_start: 0.7382 (m90) cc_final: 0.6813 (t-170) REVERT: C 212 ILE cc_start: 0.6635 (mt) cc_final: 0.6270 (mt) REVERT: D 82 ASP cc_start: 0.8984 (m-30) cc_final: 0.8648 (p0) REVERT: D 137 MET cc_start: 0.6580 (ttt) cc_final: 0.6191 (tmm) REVERT: D 235 LEU cc_start: 0.7899 (mp) cc_final: 0.7332 (mp) REVERT: D 242 TYR cc_start: 0.9124 (t80) cc_final: 0.8616 (t80) REVERT: D 262 TYR cc_start: 0.8702 (t80) cc_final: 0.8449 (t80) REVERT: E 25 TRP cc_start: 0.7885 (p-90) cc_final: 0.6817 (p-90) outliers start: 0 outliers final: 0 residues processed: 597 average time/residue: 0.1295 time to fit residues: 116.5482 Evaluate side-chains 508 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 390 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN D 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.151009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107017 restraints weight = 44798.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110970 restraints weight = 27496.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113724 restraints weight = 18668.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115483 restraints weight = 13885.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116760 restraints weight = 11075.144| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17041 Z= 0.156 Angle : 0.636 10.981 23026 Z= 0.330 Chirality : 0.043 0.188 2464 Planarity : 0.003 0.042 2931 Dihedral : 9.850 153.555 2325 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 2012 helix: 1.12 (0.15), residues: 1167 sheet: -0.44 (0.38), residues: 189 loop : 0.09 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.018 0.001 TYR D 242 PHE 0.021 0.002 PHE A 654 TRP 0.007 0.001 TRP D 30 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00347 (17038) covalent geometry : angle 0.63145 (23020) SS BOND : bond 0.00343 ( 3) SS BOND : angle 4.94058 ( 6) hydrogen bonds : bond 0.04017 ( 912) hydrogen bonds : angle 4.99332 ( 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 603 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 0.663 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 65 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 89 PHE cc_start: 0.9222 (t80) cc_final: 0.8990 (t80) REVERT: A 161 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8081 (ptm160) REVERT: A 186 ILE cc_start: 0.9547 (mm) cc_final: 0.9233 (mm) REVERT: A 188 ILE cc_start: 0.9532 (mt) cc_final: 0.9290 (mt) REVERT: A 190 MET cc_start: 0.9298 (mtm) cc_final: 0.9086 (mtm) REVERT: A 250 TYR cc_start: 0.7222 (m-80) cc_final: 0.6769 (m-80) REVERT: A 255 HIS cc_start: 0.8220 (t-90) cc_final: 0.7856 (t70) REVERT: A 257 ASP cc_start: 0.8563 (m-30) cc_final: 0.7975 (m-30) REVERT: A 263 ASP cc_start: 0.9084 (m-30) cc_final: 0.8726 (m-30) REVERT: A 290 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8831 (tm-30) REVERT: A 291 LEU cc_start: 0.9668 (mp) cc_final: 0.9165 (mt) REVERT: A 301 PHE cc_start: 0.8817 (m-80) cc_final: 0.8447 (m-80) REVERT: A 312 GLN cc_start: 0.8778 (tp40) cc_final: 0.8553 (tp40) REVERT: A 316 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 317 MET cc_start: 0.9164 (mmm) cc_final: 0.8934 (mmm) REVERT: A 322 MET cc_start: 0.8877 (mmm) cc_final: 0.8554 (mmm) REVERT: A 393 SER cc_start: 0.9169 (t) cc_final: 0.8310 (t) REVERT: A 402 GLU cc_start: 0.8306 (mp0) cc_final: 0.7582 (mp0) REVERT: A 403 ILE cc_start: 0.8467 (mm) cc_final: 0.8224 (mm) REVERT: A 447 ASN cc_start: 0.8888 (m-40) cc_final: 0.8566 (m-40) REVERT: A 501 GLN cc_start: 0.9438 (tt0) cc_final: 0.9102 (tm-30) REVERT: A 550 MET cc_start: 0.7075 (mmm) cc_final: 0.6643 (mmt) REVERT: A 571 TYR cc_start: 0.8795 (t80) cc_final: 0.8088 (t80) REVERT: A 628 GLU cc_start: 0.9259 (tt0) cc_final: 0.8908 (tt0) REVERT: A 664 THR cc_start: 0.9390 (p) cc_final: 0.8992 (p) REVERT: A 668 ASN cc_start: 0.9080 (m-40) cc_final: 0.8862 (m-40) REVERT: A 686 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7754 (mmm160) REVERT: B 10 ILE cc_start: 0.9703 (mt) cc_final: 0.9377 (tp) REVERT: B 40 TYR cc_start: 0.9200 (t80) cc_final: 0.8916 (t80) REVERT: B 99 LYS cc_start: 0.9439 (tptm) cc_final: 0.8828 (tptm) REVERT: B 106 LEU cc_start: 0.8832 (tp) cc_final: 0.8609 (tp) REVERT: B 118 TYR cc_start: 0.9022 (t80) cc_final: 0.8804 (t80) REVERT: B 129 PHE cc_start: 0.9451 (m-80) cc_final: 0.9068 (m-80) REVERT: B 150 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8938 (tp40) REVERT: B 205 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7951 (mmtm) REVERT: B 227 MET cc_start: 0.9163 (ptp) cc_final: 0.8637 (ptp) REVERT: B 274 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8195 (mmm160) REVERT: B 317 MET cc_start: 0.8444 (mtt) cc_final: 0.8126 (mpp) REVERT: B 335 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 349 LEU cc_start: 0.9576 (mt) cc_final: 0.9369 (mt) REVERT: B 352 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6944 (mm-30) REVERT: B 375 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8144 (mmmm) REVERT: B 403 ILE cc_start: 0.9136 (mm) cc_final: 0.8829 (mm) REVERT: B 431 LEU cc_start: 0.9371 (mt) cc_final: 0.9146 (mt) REVERT: B 471 TYR cc_start: 0.9239 (t80) cc_final: 0.8930 (t80) REVERT: B 475 ASN cc_start: 0.9095 (m-40) cc_final: 0.8766 (m-40) REVERT: B 550 MET cc_start: 0.7869 (mmt) cc_final: 0.7636 (mmt) REVERT: B 586 TYR cc_start: 0.9532 (m-80) cc_final: 0.9208 (m-80) REVERT: B 645 GLN cc_start: 0.9175 (tp40) cc_final: 0.8763 (tp40) REVERT: B 650 GLN cc_start: 0.6521 (mt0) cc_final: 0.5914 (mt0) REVERT: B 652 ILE cc_start: 0.9298 (mt) cc_final: 0.9086 (mt) REVERT: B 657 PHE cc_start: 0.8519 (m-80) cc_final: 0.8257 (m-80) REVERT: C 157 MET cc_start: 0.8306 (mtm) cc_final: 0.7923 (mtm) REVERT: C 200 ILE cc_start: 0.8397 (pt) cc_final: 0.8132 (pt) REVERT: C 212 ILE cc_start: 0.6353 (mt) cc_final: 0.5945 (mt) REVERT: D 74 MET cc_start: 0.6984 (tpp) cc_final: 0.6553 (ptm) REVERT: D 82 ASP cc_start: 0.8972 (m-30) cc_final: 0.8674 (p0) REVERT: D 137 MET cc_start: 0.6658 (ttt) cc_final: 0.6300 (tmm) REVERT: D 242 TYR cc_start: 0.9155 (t80) cc_final: 0.8594 (t80) REVERT: D 262 TYR cc_start: 0.8778 (t80) cc_final: 0.8536 (t80) REVERT: E 25 TRP cc_start: 0.7863 (p-90) cc_final: 0.7590 (p-90) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.1234 time to fit residues: 113.2707 Evaluate side-chains 514 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 0.0470 chunk 64 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.153683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108659 restraints weight = 45105.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112691 restraints weight = 27448.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115367 restraints weight = 18666.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116428 restraints weight = 13955.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118149 restraints weight = 11667.138| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17041 Z= 0.130 Angle : 0.632 8.799 23026 Z= 0.327 Chirality : 0.043 0.185 2464 Planarity : 0.003 0.041 2931 Dihedral : 9.552 148.952 2325 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 2012 helix: 1.15 (0.15), residues: 1168 sheet: -0.29 (0.40), residues: 173 loop : 0.06 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 446 TYR 0.017 0.001 TYR B 36 PHE 0.016 0.002 PHE D 259 TRP 0.005 0.001 TRP D 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00288 (17038) covalent geometry : angle 0.62865 (23020) SS BOND : bond 0.00587 ( 3) SS BOND : angle 4.26315 ( 6) hydrogen bonds : bond 0.03906 ( 912) hydrogen bonds : angle 4.93490 ( 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 604 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8388 (mp0) REVERT: A 95 MET cc_start: 0.8583 (mmm) cc_final: 0.8349 (mmm) REVERT: A 186 ILE cc_start: 0.9565 (mm) cc_final: 0.9291 (mm) REVERT: A 188 ILE cc_start: 0.9513 (mt) cc_final: 0.9287 (mt) REVERT: A 250 TYR cc_start: 0.7370 (m-80) cc_final: 0.6952 (m-80) REVERT: A 255 HIS cc_start: 0.8081 (t-90) cc_final: 0.7682 (t70) REVERT: A 257 ASP cc_start: 0.8651 (m-30) cc_final: 0.8163 (m-30) REVERT: A 263 ASP cc_start: 0.9110 (m-30) cc_final: 0.8718 (m-30) REVERT: A 290 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 291 LEU cc_start: 0.9626 (mp) cc_final: 0.9122 (mt) REVERT: A 301 PHE cc_start: 0.8667 (m-80) cc_final: 0.8360 (m-80) REVERT: A 312 GLN cc_start: 0.8731 (tp40) cc_final: 0.8492 (tp40) REVERT: A 322 MET cc_start: 0.8867 (mmm) cc_final: 0.8530 (mmm) REVERT: A 390 GLN cc_start: 0.8564 (mm110) cc_final: 0.8108 (mm-40) REVERT: A 393 SER cc_start: 0.9110 (t) cc_final: 0.8192 (t) REVERT: A 402 GLU cc_start: 0.8361 (mp0) cc_final: 0.7666 (mp0) REVERT: A 403 ILE cc_start: 0.8482 (mm) cc_final: 0.8259 (mm) REVERT: A 447 ASN cc_start: 0.8847 (m-40) cc_final: 0.8557 (m-40) REVERT: A 456 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8905 (mtmm) REVERT: A 474 GLN cc_start: 0.8915 (mm110) cc_final: 0.8533 (mp10) REVERT: A 493 MET cc_start: 0.8624 (ttt) cc_final: 0.8065 (ttp) REVERT: A 494 MET cc_start: 0.8387 (mmt) cc_final: 0.7864 (mmt) REVERT: A 501 GLN cc_start: 0.9439 (tt0) cc_final: 0.9065 (tm-30) REVERT: A 510 LYS cc_start: 0.9008 (tmtt) cc_final: 0.8624 (tptp) REVERT: A 571 TYR cc_start: 0.8752 (t80) cc_final: 0.7984 (t80) REVERT: A 586 TYR cc_start: 0.9200 (m-80) cc_final: 0.8564 (m-80) REVERT: A 628 GLU cc_start: 0.9261 (tt0) cc_final: 0.8952 (tt0) REVERT: A 664 THR cc_start: 0.9390 (p) cc_final: 0.9034 (p) REVERT: A 667 LEU cc_start: 0.9291 (tt) cc_final: 0.9082 (tt) REVERT: A 668 ASN cc_start: 0.9078 (m-40) cc_final: 0.8864 (m-40) REVERT: A 686 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7753 (mmm160) REVERT: B 10 ILE cc_start: 0.9698 (mt) cc_final: 0.9377 (tp) REVERT: B 40 TYR cc_start: 0.9200 (t80) cc_final: 0.8912 (t80) REVERT: B 99 LYS cc_start: 0.9457 (tptm) cc_final: 0.8937 (tptm) REVERT: B 106 LEU cc_start: 0.8760 (tp) cc_final: 0.8160 (tp) REVERT: B 118 TYR cc_start: 0.8911 (t80) cc_final: 0.8665 (t80) REVERT: B 120 ASP cc_start: 0.9306 (m-30) cc_final: 0.9073 (m-30) REVERT: B 129 PHE cc_start: 0.9431 (m-80) cc_final: 0.9029 (m-80) REVERT: B 150 GLN cc_start: 0.9198 (tp-100) cc_final: 0.8963 (tp40) REVERT: B 227 MET cc_start: 0.9149 (ptp) cc_final: 0.8617 (ptp) REVERT: B 274 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8287 (mmm160) REVERT: B 335 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 344 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8196 (mt-10) REVERT: B 349 LEU cc_start: 0.9576 (mt) cc_final: 0.9351 (mt) REVERT: B 375 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 390 GLN cc_start: 0.9267 (mt0) cc_final: 0.8996 (mm-40) REVERT: B 403 ILE cc_start: 0.9068 (mm) cc_final: 0.8804 (mm) REVERT: B 472 LEU cc_start: 0.9460 (mm) cc_final: 0.9260 (mt) REVERT: B 475 ASN cc_start: 0.9104 (m-40) cc_final: 0.8764 (m-40) REVERT: B 483 GLU cc_start: 0.9295 (pm20) cc_final: 0.9032 (pm20) REVERT: B 496 ASN cc_start: 0.9377 (t0) cc_final: 0.9038 (t0) REVERT: B 500 ILE cc_start: 0.9660 (mt) cc_final: 0.9451 (mt) REVERT: B 505 GLU cc_start: 0.9338 (pt0) cc_final: 0.9069 (pt0) REVERT: B 576 LEU cc_start: 0.9327 (mt) cc_final: 0.9111 (mt) REVERT: B 586 TYR cc_start: 0.9494 (m-80) cc_final: 0.9210 (m-80) REVERT: B 634 MET cc_start: 0.9208 (mmm) cc_final: 0.8973 (mmp) REVERT: B 645 GLN cc_start: 0.9204 (tp40) cc_final: 0.8817 (tp40) REVERT: B 650 GLN cc_start: 0.6635 (mt0) cc_final: 0.6011 (mt0) REVERT: B 657 PHE cc_start: 0.8573 (m-80) cc_final: 0.8235 (m-80) REVERT: C 157 MET cc_start: 0.7870 (mtm) cc_final: 0.7619 (mtm) REVERT: C 200 ILE cc_start: 0.8404 (pt) cc_final: 0.8012 (pt) REVERT: D 74 MET cc_start: 0.7342 (tpp) cc_final: 0.7072 (ptm) REVERT: D 82 ASP cc_start: 0.8965 (m-30) cc_final: 0.8696 (p0) REVERT: D 137 MET cc_start: 0.6680 (ttt) cc_final: 0.6412 (tmm) REVERT: D 242 TYR cc_start: 0.9118 (t80) cc_final: 0.8745 (t80) REVERT: D 262 TYR cc_start: 0.8858 (t80) cc_final: 0.8615 (t80) REVERT: E 25 TRP cc_start: 0.7837 (p-90) cc_final: 0.7559 (p-90) REVERT: E 34 MET cc_start: 0.8964 (ptt) cc_final: 0.8693 (ppp) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.1327 time to fit residues: 121.2746 Evaluate side-chains 506 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 7.9990 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS C 84 HIS C 216 GLN D 28 GLN ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100320 restraints weight = 48030.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103986 restraints weight = 29731.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106561 restraints weight = 20165.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108151 restraints weight = 15160.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109300 restraints weight = 12172.902| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 17041 Z= 0.274 Angle : 0.742 10.202 23026 Z= 0.389 Chirality : 0.046 0.191 2464 Planarity : 0.004 0.054 2931 Dihedral : 9.861 157.593 2325 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 aren not related in a simple way. whole: 0.48 (0.18), residues: 2012 helix: 0.85 (0.15), residues: 1161 sheet: -0.79 (0.38), residues: 185 loop : -0.06 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 261 TYR 0.028 0.002 TYR D 174 PHE 0.026 0.002 PHE A 378 TRP 0.018 0.002 TRP D 30 HIS 0.015 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00579 (17038) covalent geometry : angle 0.73738 (23020) SS BOND : bond 0.00609 ( 3) SS BOND : angle 5.06245 ( 6) hydrogen bonds : bond 0.04282 ( 912) hydrogen bonds : angle 5.28660 ( 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 587 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8077 (mp0) REVERT: A 128 PHE cc_start: 0.9441 (t80) cc_final: 0.9229 (t80) REVERT: A 147 GLN cc_start: 0.9017 (mt0) cc_final: 0.8694 (mt0) REVERT: A 157 LEU cc_start: 0.9281 (tp) cc_final: 0.9042 (tp) REVERT: A 161 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7293 (ptm160) REVERT: A 164 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8360 (ttm110) REVERT: A 186 ILE cc_start: 0.9557 (mm) cc_final: 0.9329 (mm) REVERT: A 190 MET cc_start: 0.9325 (mtm) cc_final: 0.8853 (mtm) REVERT: A 250 TYR cc_start: 0.7313 (m-80) cc_final: 0.6973 (m-80) REVERT: A 255 HIS cc_start: 0.8388 (t-90) cc_final: 0.7598 (t70) REVERT: A 257 ASP cc_start: 0.8547 (m-30) cc_final: 0.8094 (m-30) REVERT: A 263 ASP cc_start: 0.9043 (m-30) cc_final: 0.8698 (m-30) REVERT: A 291 LEU cc_start: 0.9605 (mp) cc_final: 0.9177 (mp) REVERT: A 312 GLN cc_start: 0.8738 (tp40) cc_final: 0.8400 (tp40) REVERT: A 317 MET cc_start: 0.8936 (mmm) cc_final: 0.8653 (mmm) REVERT: A 322 MET cc_start: 0.8820 (mmm) cc_final: 0.8451 (mmm) REVERT: A 447 ASN cc_start: 0.8820 (m-40) cc_final: 0.8559 (m-40) REVERT: A 456 LYS cc_start: 0.9240 (mtmm) cc_final: 0.8960 (mtmm) REVERT: A 501 GLN cc_start: 0.9445 (tt0) cc_final: 0.9075 (tm-30) REVERT: A 510 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8371 (tptp) REVERT: A 571 TYR cc_start: 0.8852 (t80) cc_final: 0.8382 (t80) REVERT: A 586 TYR cc_start: 0.9191 (m-80) cc_final: 0.8573 (m-80) REVERT: A 601 ILE cc_start: 0.9530 (tt) cc_final: 0.9131 (tt) REVERT: A 615 MET cc_start: 0.9003 (mmp) cc_final: 0.8563 (mmp) REVERT: A 628 GLU cc_start: 0.9280 (tt0) cc_final: 0.8990 (tt0) REVERT: A 664 THR cc_start: 0.9448 (p) cc_final: 0.9069 (p) REVERT: A 668 ASN cc_start: 0.9148 (m-40) cc_final: 0.8930 (m-40) REVERT: A 686 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7798 (mmm160) REVERT: B 10 ILE cc_start: 0.9706 (mt) cc_final: 0.9425 (tp) REVERT: B 99 LYS cc_start: 0.9530 (tptm) cc_final: 0.9184 (tptp) REVERT: B 106 LEU cc_start: 0.9094 (tp) cc_final: 0.8767 (tp) REVERT: B 120 ASP cc_start: 0.9409 (m-30) cc_final: 0.9160 (m-30) REVERT: B 129 PHE cc_start: 0.9500 (m-80) cc_final: 0.9182 (m-80) REVERT: B 167 LEU cc_start: 0.9088 (mt) cc_final: 0.8886 (mt) REVERT: B 227 MET cc_start: 0.9120 (ptp) cc_final: 0.8668 (ptp) REVERT: B 235 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.8316 (mtm-85) REVERT: B 274 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8223 (mmm160) REVERT: B 322 MET cc_start: 0.8625 (mmm) cc_final: 0.8381 (mmm) REVERT: B 335 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 375 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8227 (mmmm) REVERT: B 403 ILE cc_start: 0.9135 (mm) cc_final: 0.8829 (mm) REVERT: B 426 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8245 (mp0) REVERT: B 431 LEU cc_start: 0.9400 (mt) cc_final: 0.9184 (mt) REVERT: B 475 ASN cc_start: 0.9162 (m-40) cc_final: 0.8866 (m-40) REVERT: B 496 ASN cc_start: 0.9480 (t0) cc_final: 0.9197 (t0) REVERT: B 575 ARG cc_start: 0.8726 (ptp90) cc_final: 0.8385 (ptp-170) REVERT: B 576 LEU cc_start: 0.9236 (mt) cc_final: 0.8977 (mt) REVERT: B 586 TYR cc_start: 0.9514 (m-80) cc_final: 0.9192 (m-80) REVERT: B 599 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 602 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 645 GLN cc_start: 0.9229 (tp40) cc_final: 0.8824 (tp-100) REVERT: B 650 GLN cc_start: 0.6438 (mt0) cc_final: 0.5793 (mt0) REVERT: C 157 MET cc_start: 0.8290 (mtm) cc_final: 0.7929 (mtm) REVERT: C 200 ILE cc_start: 0.8263 (pt) cc_final: 0.8043 (pt) REVERT: C 241 GLU cc_start: 0.9286 (pt0) cc_final: 0.8995 (pt0) REVERT: D 16 ASP cc_start: 0.4901 (m-30) cc_final: 0.4485 (m-30) REVERT: D 20 MET cc_start: 0.9215 (tpp) cc_final: 0.8997 (tpp) REVERT: D 137 MET cc_start: 0.6840 (ttt) cc_final: 0.6612 (ppp) REVERT: D 242 TYR cc_start: 0.9162 (t80) cc_final: 0.8645 (t80) REVERT: D 262 TYR cc_start: 0.8990 (t80) cc_final: 0.8758 (t80) REVERT: E 25 TRP cc_start: 0.7999 (p-90) cc_final: 0.7006 (p-90) REVERT: E 34 MET cc_start: 0.8931 (ptt) cc_final: 0.8577 (ppp) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.1291 time to fit residues: 115.3921 Evaluate side-chains 492 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103420 restraints weight = 45901.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107392 restraints weight = 27949.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110031 restraints weight = 18799.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111917 restraints weight = 14008.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113193 restraints weight = 11122.389| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17041 Z= 0.168 Angle : 0.710 12.814 23026 Z= 0.363 Chirality : 0.046 0.217 2464 Planarity : 0.004 0.053 2931 Dihedral : 9.666 150.316 2325 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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 aren not related in a simple way. whole: 0.53 (0.19), residues: 2012 helix: 0.85 (0.15), residues: 1175 sheet: -0.51 (0.39), residues: 183 loop : -0.08 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 502 TYR 0.027 0.002 TYR B 498 PHE 0.028 0.002 PHE C 92 TRP 0.015 0.001 TRP D 30 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00375 (17038) covalent geometry : angle 0.70513 (23020) SS BOND : bond 0.00785 ( 3) SS BOND : angle 4.96476 ( 6) hydrogen bonds : bond 0.04069 ( 912) hydrogen bonds : angle 5.16872 ( 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 579 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8420 (mp0) REVERT: A 91 PHE cc_start: 0.8732 (m-10) cc_final: 0.8351 (m-80) REVERT: A 157 LEU cc_start: 0.9213 (tp) cc_final: 0.8954 (tp) REVERT: A 161 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7374 (ptm160) REVERT: A 164 ARG cc_start: 0.8777 (ttp80) cc_final: 0.7837 (ttp80) REVERT: A 186 ILE cc_start: 0.9568 (mm) cc_final: 0.9352 (mm) REVERT: A 188 ILE cc_start: 0.9536 (mt) cc_final: 0.9310 (mt) REVERT: A 190 MET cc_start: 0.9342 (mtm) cc_final: 0.8893 (mtm) REVERT: A 250 TYR cc_start: 0.7236 (m-80) cc_final: 0.6814 (m-80) REVERT: A 257 ASP cc_start: 0.8653 (m-30) cc_final: 0.8349 (m-30) REVERT: A 263 ASP cc_start: 0.9117 (m-30) cc_final: 0.8804 (m-30) REVERT: A 290 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 291 LEU cc_start: 0.9560 (mp) cc_final: 0.8941 (mt) REVERT: A 301 PHE cc_start: 0.8857 (m-80) cc_final: 0.8590 (m-80) REVERT: A 312 GLN cc_start: 0.8608 (tp40) cc_final: 0.8278 (tp40) REVERT: A 317 MET cc_start: 0.8929 (mmm) cc_final: 0.8628 (mmm) REVERT: A 322 MET cc_start: 0.8825 (mmm) cc_final: 0.8489 (mmm) REVERT: A 421 GLU cc_start: 0.8726 (pm20) cc_final: 0.8349 (pp20) REVERT: A 447 ASN cc_start: 0.8816 (m-40) cc_final: 0.8539 (m-40) REVERT: A 456 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8959 (mtmm) REVERT: A 474 GLN cc_start: 0.8788 (mm110) cc_final: 0.8393 (mp10) REVERT: A 493 MET cc_start: 0.8631 (ttt) cc_final: 0.8197 (ttp) REVERT: A 501 GLN cc_start: 0.9430 (tt0) cc_final: 0.9073 (tm-30) REVERT: A 510 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8617 (tptt) REVERT: A 571 TYR cc_start: 0.8792 (t80) cc_final: 0.8116 (t80) REVERT: A 586 TYR cc_start: 0.9180 (m-80) cc_final: 0.8746 (m-80) REVERT: A 598 MET cc_start: 0.8492 (mtp) cc_final: 0.8166 (ttp) REVERT: A 664 THR cc_start: 0.9441 (p) cc_final: 0.9099 (p) REVERT: A 668 ASN cc_start: 0.9102 (m-40) cc_final: 0.8885 (m-40) REVERT: A 686 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7811 (mmm160) REVERT: B 10 ILE cc_start: 0.9698 (mt) cc_final: 0.9396 (tp) REVERT: B 99 LYS cc_start: 0.9505 (tptm) cc_final: 0.9183 (tptp) REVERT: B 106 LEU cc_start: 0.8966 (tp) cc_final: 0.8738 (tp) REVERT: B 129 PHE cc_start: 0.9426 (m-80) cc_final: 0.9112 (m-80) REVERT: B 227 MET cc_start: 0.9098 (ptp) cc_final: 0.8597 (ptp) REVERT: B 235 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: B 321 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 322 MET cc_start: 0.8552 (mmm) cc_final: 0.7920 (mmm) REVERT: B 344 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 349 LEU cc_start: 0.9566 (mt) cc_final: 0.9354 (mt) REVERT: B 375 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8469 (mtpt) REVERT: B 403 ILE cc_start: 0.9093 (mm) cc_final: 0.8826 (mm) REVERT: B 426 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8644 (mp0) REVERT: B 456 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8523 (mmtm) REVERT: B 469 HIS cc_start: 0.8458 (t-170) cc_final: 0.8219 (t70) REVERT: B 475 ASN cc_start: 0.9180 (m-40) cc_final: 0.8801 (m-40) REVERT: B 479 TYR cc_start: 0.8233 (t80) cc_final: 0.7995 (t80) REVERT: B 483 GLU cc_start: 0.9342 (pm20) cc_final: 0.9136 (pm20) REVERT: B 502 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8353 (tpp80) REVERT: B 576 LEU cc_start: 0.9212 (mt) cc_final: 0.8990 (mt) REVERT: B 602 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B 645 GLN cc_start: 0.9249 (tp40) cc_final: 0.8794 (tp40) REVERT: B 650 GLN cc_start: 0.6484 (mt0) cc_final: 0.5888 (mt0) REVERT: B 657 PHE cc_start: 0.8284 (m-10) cc_final: 0.8037 (m-10) REVERT: C 157 MET cc_start: 0.8152 (mtm) cc_final: 0.7949 (mtm) REVERT: C 200 ILE cc_start: 0.8209 (pt) cc_final: 0.7799 (pt) REVERT: C 241 GLU cc_start: 0.9329 (pt0) cc_final: 0.9053 (pt0) REVERT: D 20 MET cc_start: 0.9263 (tpp) cc_final: 0.9051 (tpp) REVERT: D 242 TYR cc_start: 0.9056 (t80) cc_final: 0.8595 (t80) REVERT: D 262 TYR cc_start: 0.8920 (t80) cc_final: 0.8692 (t80) REVERT: E 25 TRP cc_start: 0.7979 (p-90) cc_final: 0.6907 (p-90) REVERT: E 34 MET cc_start: 0.8956 (ptt) cc_final: 0.8599 (ppp) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.1271 time to fit residues: 111.9361 Evaluate side-chains 498 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 194 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107680 restraints weight = 45802.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111445 restraints weight = 28181.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114037 restraints weight = 19237.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115825 restraints weight = 14317.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117056 restraints weight = 11406.070| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.7384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17041 Z= 0.147 Angle : 0.704 12.263 23026 Z= 0.363 Chirality : 0.045 0.204 2464 Planarity : 0.004 0.069 2931 Dihedral : 9.494 146.825 2325 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 2012 helix: 0.79 (0.15), residues: 1177 sheet: -0.42 (0.39), residues: 179 loop : -0.19 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 502 TYR 0.027 0.002 TYR D 105 PHE 0.023 0.002 PHE A 100 TRP 0.012 0.001 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00331 (17038) covalent geometry : angle 0.69882 (23020) SS BOND : bond 0.00581 ( 3) SS BOND : angle 5.08617 ( 6) hydrogen bonds : bond 0.04008 ( 912) hydrogen bonds : angle 5.15987 ( 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 570 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.644 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 55 LEU cc_start: 0.9687 (mm) cc_final: 0.9461 (pp) REVERT: A 65 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8423 (mp0) REVERT: A 91 PHE cc_start: 0.8724 (m-10) cc_final: 0.8517 (m-80) REVERT: A 147 GLN cc_start: 0.8967 (mt0) cc_final: 0.8491 (tt0) REVERT: A 161 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7577 (ptm160) REVERT: A 164 ARG cc_start: 0.8682 (ttp80) cc_final: 0.7783 (ttp80) REVERT: A 186 ILE cc_start: 0.9546 (mm) cc_final: 0.9327 (mm) REVERT: A 188 ILE cc_start: 0.9558 (mt) cc_final: 0.9253 (mt) REVERT: A 190 MET cc_start: 0.9335 (mtm) cc_final: 0.8868 (mtm) REVERT: A 236 TYR cc_start: 0.8966 (t80) cc_final: 0.8678 (t80) REVERT: A 250 TYR cc_start: 0.7290 (m-80) cc_final: 0.6870 (m-80) REVERT: A 257 ASP cc_start: 0.8745 (m-30) cc_final: 0.8351 (m-30) REVERT: A 263 ASP cc_start: 0.9163 (m-30) cc_final: 0.8871 (m-30) REVERT: A 290 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 291 LEU cc_start: 0.9552 (mp) cc_final: 0.8925 (mt) REVERT: A 322 MET cc_start: 0.8856 (mmm) cc_final: 0.8417 (mmm) REVERT: A 361 GLN cc_start: 0.8910 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 375 LYS cc_start: 0.8657 (mmtm) cc_final: 0.7929 (mmtm) REVERT: A 447 ASN cc_start: 0.8814 (m-40) cc_final: 0.8537 (m-40) REVERT: A 456 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8872 (mtmm) REVERT: A 474 GLN cc_start: 0.8887 (mm110) cc_final: 0.8433 (mp10) REVERT: A 493 MET cc_start: 0.8600 (ttt) cc_final: 0.7855 (ttp) REVERT: A 494 MET cc_start: 0.8355 (mmt) cc_final: 0.7792 (mmt) REVERT: A 501 GLN cc_start: 0.9426 (tt0) cc_final: 0.9053 (tm-30) REVERT: A 510 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8249 (tptt) REVERT: A 586 TYR cc_start: 0.9179 (m-80) cc_final: 0.8804 (m-80) REVERT: A 615 MET cc_start: 0.9010 (mmp) cc_final: 0.8734 (mmp) REVERT: A 664 THR cc_start: 0.9388 (p) cc_final: 0.9060 (p) REVERT: A 686 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7746 (mmm160) REVERT: B 10 ILE cc_start: 0.9693 (mt) cc_final: 0.9370 (tp) REVERT: B 99 LYS cc_start: 0.9524 (tptm) cc_final: 0.8977 (tptp) REVERT: B 120 ASP cc_start: 0.9423 (m-30) cc_final: 0.9210 (m-30) REVERT: B 129 PHE cc_start: 0.9384 (m-80) cc_final: 0.9065 (m-80) REVERT: B 167 LEU cc_start: 0.8957 (mt) cc_final: 0.8635 (mt) REVERT: B 184 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8724 (ttp-170) REVERT: B 227 MET cc_start: 0.9087 (ptp) cc_final: 0.8536 (ptp) REVERT: B 321 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 322 MET cc_start: 0.8614 (mmm) cc_final: 0.7881 (mmm) REVERT: B 335 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 344 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 348 MET cc_start: 0.8469 (tpt) cc_final: 0.7902 (tpp) REVERT: B 350 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8421 (mmm160) REVERT: B 352 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6776 (mm-30) REVERT: B 375 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8233 (mmmm) REVERT: B 390 GLN cc_start: 0.9184 (mt0) cc_final: 0.8962 (mm-40) REVERT: B 399 GLU cc_start: 0.8921 (tp30) cc_final: 0.8386 (tp30) REVERT: B 403 ILE cc_start: 0.9054 (mm) cc_final: 0.8488 (tp) REVERT: B 475 ASN cc_start: 0.9205 (m-40) cc_final: 0.8816 (m-40) REVERT: B 483 GLU cc_start: 0.9346 (pm20) cc_final: 0.9120 (pm20) REVERT: B 502 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8510 (tpp80) REVERT: B 576 LEU cc_start: 0.9245 (mt) cc_final: 0.9001 (mt) REVERT: B 602 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 645 GLN cc_start: 0.9256 (tp40) cc_final: 0.8697 (tp40) REVERT: B 650 GLN cc_start: 0.6478 (mt0) cc_final: 0.5857 (mt0) REVERT: B 657 PHE cc_start: 0.8146 (m-10) cc_final: 0.7898 (m-10) REVERT: B 673 TYR cc_start: 0.8832 (t80) cc_final: 0.7797 (t80) REVERT: B 677 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8103 (mmm-85) REVERT: C 56 MET cc_start: -0.0793 (ppp) cc_final: -0.1014 (ppp) REVERT: C 157 MET cc_start: 0.8107 (mtm) cc_final: 0.7825 (mtm) REVERT: C 212 ILE cc_start: 0.5367 (mm) cc_final: 0.5130 (mm) REVERT: D 16 ASP cc_start: 0.4926 (m-30) cc_final: 0.4425 (m-30) REVERT: D 20 MET cc_start: 0.9252 (tpp) cc_final: 0.9036 (tpp) REVERT: D 233 ASN cc_start: 0.8684 (m110) cc_final: 0.8475 (m-40) REVERT: D 262 TYR cc_start: 0.8945 (t80) cc_final: 0.8736 (t80) REVERT: E 25 TRP cc_start: 0.7951 (p-90) cc_final: 0.6661 (p-90) REVERT: E 34 MET cc_start: 0.8917 (ptt) cc_final: 0.8545 (ppp) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.1291 time to fit residues: 111.8221 Evaluate side-chains 496 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 475 ASN A 647 HIS B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 233 ASN E 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.149106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106051 restraints weight = 45273.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109672 restraints weight = 27753.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112230 restraints weight = 19014.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113798 restraints weight = 14220.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115174 restraints weight = 11488.099| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7518 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= 0.164 Angle : 0.706 11.948 23026 Z= 0.364 Chirality : 0.045 0.194 2464 Planarity : 0.004 0.071 2931 Dihedral : 9.452 148.193 2325 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2012 helix: 0.76 (0.15), residues: 1164 sheet: -0.44 (0.39), residues: 178 loop : -0.27 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 502 TYR 0.025 0.002 TYR B 498 PHE 0.024 0.002 PHE D 122 TRP 0.013 0.001 TRP D 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00364 (17038) covalent geometry : angle 0.70112 (23020) SS BOND : bond 0.00891 ( 3) SS BOND : angle 5.13850 ( 6) hydrogen bonds : bond 0.03986 ( 912) hydrogen bonds : angle 5.14000 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.48 seconds wall clock time: 64 minutes 29.49 seconds (3869.49 seconds total)