Starting phenix.real_space_refine on Sat Jun 14 20:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxx_45014/06_2025/9bxx_45014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxx_45014/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxx_45014/06_2025/9bxx_45014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxx_45014/06_2025/9bxx_45014.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxx_45014/06_2025/9bxx_45014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxx_45014/06_2025/9bxx_45014.cif" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.64, per 1000 atoms: 0.64 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: 5.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.21 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: 7.65 Time building geometry restraints manager: 5.70 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: 21.920 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.820 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.620 ------------------------------------------------------------------------------- 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 : 9.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.078 0.006 TRP E 25 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE D 92 TYR 0.029 0.002 TYR E 67 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.16740 ( 912) hydrogen bonds : angle 6.70338 ( 2664) SS BOND : bond 0.36353 ( 3) SS BOND : angle 6.09121 ( 6) covalent geometry : bond 0.00603 (17038) covalent geometry : angle 0.82349 (23020) *********************** 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 : 1.990 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: A 18 ILE cc_start: 0.8493 (mt) cc_final: 0.8239 (mm) REVERT: A 99 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8869 (mmmm) REVERT: A 147 GLN cc_start: 0.8226 (mt0) cc_final: 0.7780 (mt0) REVERT: A 181 ASP cc_start: 0.8683 (m-30) cc_final: 0.8355 (m-30) REVERT: A 188 ILE cc_start: 0.8849 (mt) cc_final: 0.8403 (mt) REVERT: A 213 ILE cc_start: 0.7163 (mt) cc_final: 0.6926 (tp) REVERT: A 216 VAL cc_start: 0.8023 (p) cc_final: 0.7794 (m) REVERT: A 257 ASP cc_start: 0.8033 (m-30) cc_final: 0.7789 (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: 0.7829 (tmm) REVERT: A 500 ILE cc_start: 0.9119 (mt) cc_final: 0.8769 (mt) REVERT: A 501 GLN cc_start: 0.8436 (tt0) cc_final: 0.8059 (tt0) REVERT: A 506 ILE cc_start: 0.8783 (mt) cc_final: 0.8470 (mt) REVERT: A 594 VAL cc_start: 0.8429 (m) cc_final: 0.8180 (m) REVERT: A 630 TYR cc_start: 0.6513 (m-80) cc_final: 0.5167 (m-80) REVERT: A 644 ILE cc_start: 0.9047 (mt) cc_final: 0.8665 (mt) REVERT: B 68 PHE cc_start: 0.8403 (p90) cc_final: 0.7985 (p90) REVERT: B 69 LEU cc_start: 0.8205 (mt) cc_final: 0.7917 (mt) REVERT: B 87 LYS cc_start: 0.8400 (tptp) cc_final: 0.8121 (tptp) REVERT: B 172 LEU cc_start: 0.8956 (mp) cc_final: 0.8664 (mp) REVERT: B 175 VAL cc_start: 0.9060 (t) cc_final: 0.8812 (t) REVERT: B 204 SER cc_start: 0.8686 (m) cc_final: 0.7711 (t) REVERT: B 257 ASP cc_start: 0.8565 (m-30) cc_final: 0.7955 (m-30) REVERT: B 258 ILE cc_start: 0.8603 (tp) cc_final: 0.8392 (tp) REVERT: B 277 THR cc_start: 0.7976 (p) cc_final: 0.7403 (p) REVERT: B 322 MET cc_start: 0.7121 (mmm) cc_final: 0.6126 (mmt) REVERT: B 349 LEU cc_start: 0.8910 (mt) cc_final: 0.8691 (mt) REVERT: B 391 VAL cc_start: 0.9041 (p) cc_final: 0.8783 (p) REVERT: B 468 LEU cc_start: 0.8582 (tp) cc_final: 0.8345 (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: 0.7567 (tmm) REVERT: B 550 MET cc_start: 0.7183 (mtm) cc_final: 0.6879 (mtp) REVERT: B 565 VAL cc_start: 0.9021 (t) cc_final: 0.8600 (m) REVERT: B 574 TYR cc_start: 0.7844 (m-80) cc_final: 0.7533 (m-80) REVERT: B 575 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7350 (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: 0.8315 (m) REVERT: B 645 GLN cc_start: 0.8022 (tp40) cc_final: 0.7684 (tp40) REVERT: B 658 LEU cc_start: 0.8882 (mt) cc_final: 0.8635 (mp) REVERT: B 664 THR cc_start: 0.8929 (p) cc_final: 0.8565 (t) REVERT: C 33 GLU cc_start: 0.1904 (mp0) cc_final: 0.1278 (tm-30) REVERT: C 153 LEU cc_start: 0.6439 (tp) cc_final: 0.6130 (tp) REVERT: C 201 HIS cc_start: 0.3596 (m170) cc_final: 0.2525 (m170) REVERT: C 316 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6715 (mtmm) REVERT: D 63 THR cc_start: 0.5201 (m) cc_final: 0.4941 (m) REVERT: D 286 VAL cc_start: 0.3482 (t) cc_final: 0.2956 (p) REVERT: E 78 LEU cc_start: 0.6809 (mp) cc_final: 0.6309 (mp) outliers start: 25 outliers final: 3 residues processed: 874 average time/residue: 0.4264 time to fit residues: 550.4877 Evaluate side-chains 578 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 574 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 61 ASN B 304 HIS B 320 ASN B 370 ASN B 447 ASN B 645 GLN C 24 GLN C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111750 restraints weight = 41840.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116004 restraints weight = 25711.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118897 restraints weight = 17648.707| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17041 Z= 0.181 Angle : 0.676 13.084 23026 Z= 0.356 Chirality : 0.044 0.235 2464 Planarity : 0.004 0.054 2931 Dihedral : 10.648 155.197 2325 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.34 % Allowed : 3.13 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2012 helix: 1.24 (0.15), residues: 1151 sheet: -0.44 (0.35), residues: 187 loop : 0.37 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.009 0.002 HIS D 80 PHE 0.029 0.002 PHE C 320 TYR 0.035 0.002 TYR B 36 ARG 0.005 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 912) hydrogen bonds : angle 5.16194 ( 2664) SS BOND : bond 0.01047 ( 3) SS BOND : angle 6.80720 ( 6) covalent geometry : bond 0.00392 (17038) covalent geometry : angle 0.66668 (23020) *********************** 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 675 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 669 time to evaluate : 1.968 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: A 81 PHE cc_start: 0.9315 (m-80) cc_final: 0.9101 (m-80) REVERT: A 99 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9287 (tppp) REVERT: A 142 ASN cc_start: 0.9297 (m-40) cc_final: 0.9000 (m110) REVERT: A 186 ILE cc_start: 0.9536 (mm) cc_final: 0.9312 (mm) REVERT: A 188 ILE cc_start: 0.9603 (mt) cc_final: 0.9271 (mt) REVERT: A 190 MET cc_start: 0.9297 (mtm) cc_final: 0.9001 (mtm) REVERT: A 250 TYR cc_start: 0.7145 (m-80) cc_final: 0.6667 (m-80) REVERT: A 257 ASP cc_start: 0.8648 (m-30) cc_final: 0.7970 (m-30) REVERT: A 262 LEU cc_start: 0.9637 (mt) cc_final: 0.9427 (mt) REVERT: A 263 ASP cc_start: 0.9000 (m-30) cc_final: 0.8579 (m-30) REVERT: A 286 ASP cc_start: 0.9044 (m-30) cc_final: 0.8802 (m-30) REVERT: A 301 PHE cc_start: 0.8859 (m-80) cc_final: 0.8223 (m-10) REVERT: A 342 LEU cc_start: 0.9637 (tp) cc_final: 0.9417 (tp) REVERT: A 361 GLN cc_start: 0.8826 (tt0) cc_final: 0.8372 (tp40) REVERT: A 362 ASP cc_start: 0.8299 (m-30) cc_final: 0.7899 (m-30) REVERT: A 466 MET cc_start: 0.9013 (ptt) cc_final: 0.8713 (ptt) REVERT: A 474 GLN cc_start: 0.8737 (mt0) cc_final: 0.8500 (mt0) REVERT: A 475 ASN cc_start: 0.8769 (m-40) cc_final: 0.8318 (m110) REVERT: A 501 GLN cc_start: 0.9389 (tt0) cc_final: 0.9017 (tm-30) REVERT: A 630 TYR cc_start: 0.7089 (m-80) cc_final: 0.5321 (m-80) REVERT: A 645 GLN cc_start: 0.8490 (tp40) cc_final: 0.7802 (tp40) REVERT: A 664 THR cc_start: 0.9285 (p) cc_final: 0.8724 (p) REVERT: A 668 ASN cc_start: 0.8949 (m-40) cc_final: 0.8342 (m-40) REVERT: A 673 TYR cc_start: 0.9078 (t80) cc_final: 0.8565 (t80) REVERT: A 686 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7251 (mmm160) REVERT: B 18 ILE cc_start: 0.9241 (mm) cc_final: 0.9027 (pt) REVERT: B 23 LYS cc_start: 0.9388 (mmtm) cc_final: 0.9062 (mmtm) REVERT: B 128 PHE cc_start: 0.9604 (t80) cc_final: 0.9382 (t80) REVERT: B 144 MET cc_start: 0.9317 (mtm) cc_final: 0.8372 (mtm) REVERT: B 145 ILE cc_start: 0.9424 (tp) cc_final: 0.9175 (tp) REVERT: B 172 LEU cc_start: 0.8830 (mp) cc_final: 0.8504 (mp) REVERT: B 179 LEU cc_start: 0.9606 (tp) cc_final: 0.9397 (tp) REVERT: B 184 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8561 (mtm-85) REVERT: B 186 ILE cc_start: 0.9726 (mt) cc_final: 0.9503 (mt) REVERT: B 190 MET cc_start: 0.9386 (mtm) cc_final: 0.8902 (mtm) REVERT: B 250 TYR cc_start: 0.8265 (m-80) cc_final: 0.7956 (m-80) REVERT: B 296 LYS cc_start: 0.8784 (mmpt) cc_final: 0.8442 (tptt) REVERT: B 335 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 348 MET cc_start: 0.8498 (tpt) cc_final: 0.8291 (tpp) REVERT: B 355 TYR cc_start: 0.8823 (m-80) cc_final: 0.8571 (m-10) REVERT: B 370 ASN cc_start: 0.9261 (m-40) cc_final: 0.9026 (m110) REVERT: B 375 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8139 (mmmm) REVERT: B 390 GLN cc_start: 0.9210 (mt0) cc_final: 0.8936 (mm-40) REVERT: B 403 ILE cc_start: 0.9245 (mm) cc_final: 0.8975 (mm) REVERT: B 408 SER cc_start: 0.9240 (m) cc_final: 0.8919 (t) REVERT: B 477 ILE cc_start: 0.8488 (mm) cc_final: 0.8222 (mp) REVERT: B 493 MET cc_start: 0.9324 (tmm) cc_final: 0.9119 (tmm) REVERT: B 496 ASN cc_start: 0.9360 (t0) cc_final: 0.8769 (t0) REVERT: B 500 ILE cc_start: 0.9325 (mt) cc_final: 0.8983 (mt) REVERT: B 501 GLN cc_start: 0.9558 (tt0) cc_final: 0.9297 (tt0) REVERT: B 516 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8603 (tp40) REVERT: B 550 MET cc_start: 0.7654 (mtm) cc_final: 0.7296 (mtp) REVERT: B 586 TYR cc_start: 0.9482 (m-80) cc_final: 0.8976 (m-80) REVERT: B 604 ARG cc_start: 0.9284 (mmp80) cc_final: 0.9028 (mmp80) REVERT: B 626 TYR cc_start: 0.8303 (m-80) cc_final: 0.7909 (m-10) REVERT: B 640 MET cc_start: 0.9030 (tpp) cc_final: 0.8652 (tpp) REVERT: B 645 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8900 (tp-100) REVERT: B 656 LEU cc_start: 0.9445 (mt) cc_final: 0.9078 (mt) REVERT: B 664 THR cc_start: 0.8821 (p) cc_final: 0.8414 (t) REVERT: B 686 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8034 (mmm160) REVERT: C 33 GLU cc_start: 0.4434 (mp0) cc_final: 0.3771 (tm-30) REVERT: C 157 MET cc_start: 0.8579 (mtm) cc_final: 0.8087 (mtm) REVERT: C 162 TYR cc_start: 0.7679 (m-80) cc_final: 0.7438 (m-10) REVERT: C 177 TYR cc_start: 0.8969 (t80) cc_final: 0.8608 (t80) REVERT: D 82 ASP cc_start: 0.8803 (m-30) cc_final: 0.7954 (p0) REVERT: D 137 MET cc_start: 0.5739 (ttt) cc_final: 0.5105 (tmm) REVERT: D 227 PHE cc_start: 0.7010 (t80) cc_final: 0.6670 (t80) REVERT: D 230 ASP cc_start: 0.8947 (t70) cc_final: 0.8407 (m-30) REVERT: D 242 TYR cc_start: 0.8871 (t80) cc_final: 0.8512 (t80) REVERT: D 262 TYR cc_start: 0.8364 (t80) cc_final: 0.8115 (t80) REVERT: D 269 MET cc_start: -0.3188 (mmp) cc_final: -0.3424 (mmp) outliers start: 6 outliers final: 3 residues processed: 672 average time/residue: 0.2913 time to fit residues: 290.3407 Evaluate side-chains 537 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 534 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 312 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 475 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 313 HIS ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 69 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN ** D 238 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.157931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110957 restraints weight = 43585.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115164 restraints weight = 26999.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117642 restraints weight = 18427.665| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17041 Z= 0.148 Angle : 0.619 8.345 23026 Z= 0.325 Chirality : 0.043 0.212 2464 Planarity : 0.004 0.050 2931 Dihedral : 10.351 151.750 2325 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.06 % Allowed : 2.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2012 helix: 1.32 (0.15), residues: 1143 sheet: 0.16 (0.41), residues: 153 loop : 0.21 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 558 HIS 0.014 0.001 HIS C 201 PHE 0.032 0.002 PHE A 492 TYR 0.030 0.002 TYR A 574 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 912) hydrogen bonds : angle 4.93571 ( 2664) SS BOND : bond 0.01036 ( 3) SS BOND : angle 3.55270 ( 6) covalent geometry : bond 0.00318 (17038) covalent geometry : angle 0.61598 (23020) *********************** 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 638 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 637 time to evaluate : 1.702 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 12 LEU cc_start: 0.9678 (mt) cc_final: 0.9472 (mt) REVERT: A 31 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9061 (mp0) REVERT: A 89 PHE cc_start: 0.9104 (t80) cc_final: 0.8836 (t80) REVERT: A 91 PHE cc_start: 0.8851 (m-80) cc_final: 0.8562 (m-80) REVERT: A 119 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8284 (mt0) REVERT: A 186 ILE cc_start: 0.9532 (mm) cc_final: 0.9239 (mm) REVERT: A 188 ILE cc_start: 0.9543 (mt) cc_final: 0.9205 (mt) REVERT: A 190 MET cc_start: 0.9295 (mtm) cc_final: 0.8994 (mtm) REVERT: A 250 TYR cc_start: 0.7309 (m-80) cc_final: 0.6881 (m-80) REVERT: A 257 ASP cc_start: 0.8474 (m-30) cc_final: 0.7887 (m-30) REVERT: A 263 ASP cc_start: 0.9115 (m-30) cc_final: 0.8721 (m-30) REVERT: A 290 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9034 (tm-30) REVERT: A 291 LEU cc_start: 0.9603 (mt) cc_final: 0.9217 (mt) REVERT: A 301 PHE cc_start: 0.8884 (m-80) cc_final: 0.8360 (m-80) REVERT: A 312 GLN cc_start: 0.8615 (tp-100) cc_final: 0.8289 (tp40) REVERT: A 316 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 342 LEU cc_start: 0.9632 (tp) cc_final: 0.9432 (tp) REVERT: A 362 ASP cc_start: 0.8398 (m-30) cc_final: 0.7832 (m-30) REVERT: A 375 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8533 (mmtm) REVERT: A 475 ASN cc_start: 0.8898 (m110) cc_final: 0.8586 (m110) REVERT: A 501 GLN cc_start: 0.9456 (tt0) cc_final: 0.9016 (tm-30) REVERT: A 515 ASP cc_start: 0.9238 (m-30) cc_final: 0.9011 (m-30) REVERT: A 586 TYR cc_start: 0.9098 (m-80) cc_final: 0.8648 (m-80) REVERT: A 588 GLN cc_start: 0.9000 (mm-40) cc_final: 0.7559 (mm-40) REVERT: A 590 SER cc_start: 0.9042 (t) cc_final: 0.8525 (p) REVERT: A 615 MET cc_start: 0.8936 (mmp) cc_final: 0.8723 (mmp) REVERT: A 630 TYR cc_start: 0.7750 (m-80) cc_final: 0.6371 (m-80) REVERT: A 645 GLN cc_start: 0.8464 (tp40) cc_final: 0.8067 (tp40) REVERT: A 650 GLN cc_start: 0.8385 (mt0) cc_final: 0.7608 (mt0) REVERT: A 664 THR cc_start: 0.9387 (p) cc_final: 0.8841 (p) REVERT: A 668 ASN cc_start: 0.8810 (m-40) cc_final: 0.8371 (m-40) REVERT: A 673 TYR cc_start: 0.9159 (t80) cc_final: 0.8630 (t80) REVERT: A 686 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7853 (tpt170) REVERT: B 23 LYS cc_start: 0.9298 (mmtm) cc_final: 0.8875 (mmmt) REVERT: B 99 LYS cc_start: 0.9381 (tptm) cc_final: 0.9129 (tptm) REVERT: B 128 PHE cc_start: 0.9665 (t80) cc_final: 0.9435 (t80) REVERT: B 149 TYR cc_start: 0.9081 (t80) cc_final: 0.7934 (t80) REVERT: B 167 LEU cc_start: 0.8921 (mt) cc_final: 0.8681 (mt) REVERT: B 172 LEU cc_start: 0.8776 (mp) cc_final: 0.8472 (mp) REVERT: B 186 ILE cc_start: 0.9738 (mt) cc_final: 0.9470 (mt) REVERT: B 190 MET cc_start: 0.9395 (mtm) cc_final: 0.9148 (mtm) REVERT: B 235 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8150 (mtm-85) REVERT: B 296 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8434 (tptt) REVERT: B 317 MET cc_start: 0.8601 (mtt) cc_final: 0.8181 (mpp) REVERT: B 319 MET cc_start: 0.8535 (tpp) cc_final: 0.8068 (tpp) REVERT: B 322 MET cc_start: 0.8208 (mmt) cc_final: 0.7852 (mmm) REVERT: B 349 LEU cc_start: 0.9584 (mt) cc_final: 0.9372 (mt) REVERT: B 355 TYR cc_start: 0.8917 (m-80) cc_final: 0.8669 (m-10) REVERT: B 370 ASN cc_start: 0.9402 (m-40) cc_final: 0.9157 (m110) REVERT: B 375 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8265 (mtpt) REVERT: B 403 ILE cc_start: 0.9281 (mm) cc_final: 0.9049 (mm) REVERT: B 430 LYS cc_start: 0.8886 (mttt) cc_final: 0.8513 (mmtt) REVERT: B 493 MET cc_start: 0.9320 (tmm) cc_final: 0.9004 (tmm) REVERT: B 501 GLN cc_start: 0.9547 (tt0) cc_final: 0.9254 (tt0) REVERT: B 602 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 604 ARG cc_start: 0.9279 (mmp80) cc_final: 0.9025 (mmp80) REVERT: B 626 TYR cc_start: 0.7845 (m-80) cc_final: 0.7284 (m-80) REVERT: B 640 MET cc_start: 0.9024 (tpp) cc_final: 0.8712 (tpp) REVERT: B 645 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8829 (tp-100) REVERT: C 157 MET cc_start: 0.8292 (mtm) cc_final: 0.7727 (mtm) REVERT: C 177 TYR cc_start: 0.8919 (t80) cc_final: 0.8608 (t80) REVERT: D 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.7989 (p0) REVERT: D 116 GLU cc_start: 0.9427 (pm20) cc_final: 0.9025 (tm-30) REVERT: D 137 MET cc_start: 0.6046 (ttt) cc_final: 0.5577 (tmm) REVERT: D 185 MET cc_start: 0.4456 (mmp) cc_final: 0.4155 (mmm) REVERT: D 230 ASP cc_start: 0.8958 (t70) cc_final: 0.8387 (m-30) REVERT: D 242 TYR cc_start: 0.8955 (t80) cc_final: 0.8735 (t80) REVERT: D 262 TYR cc_start: 0.8633 (t80) cc_final: 0.8376 (t80) REVERT: E 25 TRP cc_start: 0.8162 (p-90) cc_final: 0.7375 (p-90) REVERT: E 34 MET cc_start: 0.9000 (mpp) cc_final: 0.8758 (ptp) outliers start: 1 outliers final: 0 residues processed: 637 average time/residue: 0.3096 time to fit residues: 294.0232 Evaluate side-chains 540 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 197 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 142 ASN B 180 ASN B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 84 HIS C 132 GLN C 238 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099454 restraints weight = 46052.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103040 restraints weight = 28296.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105496 restraints weight = 19265.141| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 17041 Z= 0.276 Angle : 0.723 11.340 23026 Z= 0.380 Chirality : 0.045 0.183 2464 Planarity : 0.005 0.059 2931 Dihedral : 10.669 159.570 2325 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2012 helix: 1.02 (0.15), residues: 1160 sheet: -0.45 (0.36), residues: 189 loop : 0.21 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 623 HIS 0.012 0.002 HIS C 201 PHE 0.027 0.002 PHE B 129 TYR 0.035 0.002 TYR C 174 ARG 0.008 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 912) hydrogen bonds : angle 5.17326 ( 2664) SS BOND : bond 0.00912 ( 3) SS BOND : angle 5.59712 ( 6) covalent geometry : bond 0.00577 (17038) covalent geometry : angle 0.71773 (23020) *********************** 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 616 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 614 time to evaluate : 1.780 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: A 81 PHE cc_start: 0.9449 (m-80) cc_final: 0.9092 (m-80) REVERT: A 89 PHE cc_start: 0.9371 (t80) cc_final: 0.9155 (t80) REVERT: A 128 PHE cc_start: 0.9470 (t80) cc_final: 0.9270 (t80) REVERT: A 157 LEU cc_start: 0.9200 (tp) cc_final: 0.8914 (tp) REVERT: A 186 ILE cc_start: 0.9554 (mm) cc_final: 0.9145 (mm) REVERT: A 190 MET cc_start: 0.9251 (mtm) cc_final: 0.8991 (mtm) REVERT: A 250 TYR cc_start: 0.7355 (m-80) cc_final: 0.7042 (m-80) REVERT: A 257 ASP cc_start: 0.8437 (m-30) cc_final: 0.8032 (m-30) REVERT: A 262 LEU cc_start: 0.9661 (mt) cc_final: 0.9452 (mt) REVERT: A 263 ASP cc_start: 0.8929 (m-30) cc_final: 0.8614 (m-30) REVERT: A 286 ASP cc_start: 0.9124 (m-30) cc_final: 0.8906 (m-30) REVERT: A 290 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8914 (tm-30) REVERT: A 291 LEU cc_start: 0.9736 (mt) cc_final: 0.9283 (mt) REVERT: A 301 PHE cc_start: 0.8918 (m-80) cc_final: 0.8425 (m-80) REVERT: A 312 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8222 (tp40) REVERT: A 314 MET cc_start: 0.8938 (tmm) cc_final: 0.8522 (tmm) REVERT: A 317 MET cc_start: 0.9155 (mmm) cc_final: 0.8921 (mmm) REVERT: A 319 MET cc_start: 0.9010 (tpp) cc_final: 0.8716 (tpt) REVERT: A 322 MET cc_start: 0.8762 (mmm) cc_final: 0.8549 (mmm) REVERT: A 362 ASP cc_start: 0.8395 (m-30) cc_final: 0.7911 (m-30) REVERT: A 367 VAL cc_start: 0.9591 (m) cc_final: 0.9362 (p) REVERT: A 425 ILE cc_start: 0.9307 (mt) cc_final: 0.8955 (mm) REVERT: A 494 MET cc_start: 0.8345 (mmt) cc_final: 0.7958 (mmt) REVERT: A 501 GLN cc_start: 0.9512 (tt0) cc_final: 0.9165 (tm-30) REVERT: A 586 TYR cc_start: 0.9107 (m-80) cc_final: 0.8502 (m-80) REVERT: A 590 SER cc_start: 0.9077 (t) cc_final: 0.8592 (t) REVERT: A 615 MET cc_start: 0.8981 (mmp) cc_final: 0.8699 (mmp) REVERT: A 645 GLN cc_start: 0.8627 (tp40) cc_final: 0.8404 (tp40) REVERT: A 664 THR cc_start: 0.9428 (p) cc_final: 0.9002 (p) REVERT: A 668 ASN cc_start: 0.9023 (m-40) cc_final: 0.8736 (m-40) REVERT: A 686 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7793 (mmm160) REVERT: B 95 MET cc_start: 0.8767 (mmp) cc_final: 0.8488 (mpp) REVERT: B 99 LYS cc_start: 0.9402 (tptm) cc_final: 0.9097 (tptp) REVERT: B 129 PHE cc_start: 0.9423 (m-80) cc_final: 0.8951 (m-80) REVERT: B 139 GLU cc_start: 0.9116 (pm20) cc_final: 0.8827 (pm20) REVERT: B 167 LEU cc_start: 0.9069 (mt) cc_final: 0.8793 (mt) REVERT: B 172 LEU cc_start: 0.8964 (mp) cc_final: 0.8742 (mp) REVERT: B 186 ILE cc_start: 0.9675 (mt) cc_final: 0.9461 (mt) REVERT: B 190 MET cc_start: 0.9369 (mtm) cc_final: 0.9144 (mtm) REVERT: B 205 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8070 (mmmm) REVERT: B 315 ASP cc_start: 0.8590 (p0) cc_final: 0.7924 (p0) REVERT: B 317 MET cc_start: 0.8515 (mtt) cc_final: 0.8209 (mpp) REVERT: B 322 MET cc_start: 0.8283 (mmt) cc_final: 0.8007 (mmm) REVERT: B 370 ASN cc_start: 0.9507 (m-40) cc_final: 0.9240 (m110) REVERT: B 375 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8346 (mtpt) REVERT: B 377 LYS cc_start: 0.7778 (mttt) cc_final: 0.7436 (mttp) REVERT: B 403 ILE cc_start: 0.9235 (mm) cc_final: 0.9000 (mm) REVERT: B 570 MET cc_start: 0.9087 (tpp) cc_final: 0.8320 (tpp) REVERT: B 598 MET cc_start: 0.8787 (ttm) cc_final: 0.8553 (ttm) REVERT: B 602 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 604 ARG cc_start: 0.9360 (mmp80) cc_final: 0.8883 (mmp80) REVERT: B 640 MET cc_start: 0.9037 (tpp) cc_final: 0.8766 (tpp) REVERT: B 645 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8764 (tp-100) REVERT: C 130 TYR cc_start: 0.9010 (m-80) cc_final: 0.8598 (m-80) REVERT: C 157 MET cc_start: 0.8655 (mtm) cc_final: 0.8154 (mtm) REVERT: C 177 TYR cc_start: 0.8851 (t80) cc_final: 0.8570 (t80) REVERT: C 200 ILE cc_start: 0.8435 (pt) cc_final: 0.8213 (pt) REVERT: D 82 ASP cc_start: 0.8971 (m-30) cc_final: 0.8607 (p0) REVERT: D 116 GLU cc_start: 0.9394 (pm20) cc_final: 0.9019 (tm-30) REVERT: D 117 THR cc_start: 0.9406 (p) cc_final: 0.9128 (p) REVERT: D 137 MET cc_start: 0.6618 (ttt) cc_final: 0.6247 (tmm) REVERT: D 185 MET cc_start: 0.3732 (mmp) cc_final: 0.3459 (mpp) REVERT: D 230 ASP cc_start: 0.8940 (t70) cc_final: 0.8386 (m-30) REVERT: D 242 TYR cc_start: 0.9111 (t80) cc_final: 0.8520 (t80) REVERT: D 262 TYR cc_start: 0.8774 (t80) cc_final: 0.8450 (t80) REVERT: E 25 TRP cc_start: 0.8484 (p-90) cc_final: 0.7744 (p-90) outliers start: 2 outliers final: 1 residues processed: 616 average time/residue: 0.2895 time to fit residues: 266.6786 Evaluate side-chains 518 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 232 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 475 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.149511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104955 restraints weight = 45284.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108847 restraints weight = 27301.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111453 restraints weight = 18563.639| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17041 Z= 0.146 Angle : 0.641 12.688 23026 Z= 0.331 Chirality : 0.044 0.194 2464 Planarity : 0.004 0.074 2931 Dihedral : 10.240 150.391 2325 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2012 helix: 1.12 (0.15), residues: 1138 sheet: -0.58 (0.37), residues: 195 loop : 0.15 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.007 0.001 HIS D 201 PHE 0.027 0.002 PHE D 168 TYR 0.027 0.002 TYR A 574 ARG 0.019 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 912) hydrogen bonds : angle 4.92374 ( 2664) SS BOND : bond 0.01828 ( 3) SS BOND : angle 3.48614 ( 6) covalent geometry : bond 0.00320 (17038) covalent geometry : angle 0.63891 (23020) *********************** 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 613 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 612 time to evaluate : 1.901 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 54 LYS cc_start: 0.9629 (tttt) cc_final: 0.8710 (ttpt) REVERT: A 117 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8616 (mtt90) REVERT: A 186 ILE cc_start: 0.9543 (mm) cc_final: 0.9202 (mm) REVERT: A 250 TYR cc_start: 0.7155 (m-80) cc_final: 0.6715 (m-80) REVERT: A 257 ASP cc_start: 0.8526 (m-30) cc_final: 0.7999 (m-30) REVERT: A 263 ASP cc_start: 0.8958 (m-30) cc_final: 0.8667 (m-30) REVERT: A 286 ASP cc_start: 0.9122 (m-30) cc_final: 0.8907 (m-30) REVERT: A 290 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8683 (tm-30) REVERT: A 291 LEU cc_start: 0.9699 (mt) cc_final: 0.9280 (mt) REVERT: A 301 PHE cc_start: 0.8791 (m-80) cc_final: 0.8404 (m-80) REVERT: A 312 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8014 (tp40) REVERT: A 314 MET cc_start: 0.8795 (tmm) cc_final: 0.8255 (tmm) REVERT: A 316 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 317 MET cc_start: 0.9190 (mmm) cc_final: 0.8807 (mmm) REVERT: A 322 MET cc_start: 0.8823 (mmm) cc_final: 0.8538 (mmm) REVERT: A 362 ASP cc_start: 0.8337 (m-30) cc_final: 0.7894 (m-30) REVERT: A 375 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8477 (mmtm) REVERT: A 393 SER cc_start: 0.9153 (t) cc_final: 0.8329 (t) REVERT: A 402 GLU cc_start: 0.8214 (mp0) cc_final: 0.7568 (mp0) REVERT: A 494 MET cc_start: 0.8442 (mmt) cc_final: 0.7916 (mmt) REVERT: A 501 GLN cc_start: 0.9477 (tt0) cc_final: 0.9119 (tm-30) REVERT: A 586 TYR cc_start: 0.9160 (m-80) cc_final: 0.8443 (m-80) REVERT: A 615 MET cc_start: 0.8998 (mmp) cc_final: 0.8709 (mmp) REVERT: A 628 GLU cc_start: 0.9388 (tt0) cc_final: 0.8973 (mm-30) REVERT: A 645 GLN cc_start: 0.8594 (tp40) cc_final: 0.8378 (tp40) REVERT: A 650 GLN cc_start: 0.8455 (mt0) cc_final: 0.7514 (mt0) REVERT: A 664 THR cc_start: 0.9440 (p) cc_final: 0.9076 (p) REVERT: A 667 LEU cc_start: 0.9318 (tt) cc_final: 0.9108 (tt) REVERT: A 668 ASN cc_start: 0.9001 (m-40) cc_final: 0.8788 (m-40) REVERT: A 686 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7712 (mmm160) REVERT: B 99 LYS cc_start: 0.9333 (tptm) cc_final: 0.9022 (tptp) REVERT: B 129 PHE cc_start: 0.9418 (m-80) cc_final: 0.8963 (m-80) REVERT: B 139 GLU cc_start: 0.9042 (pm20) cc_final: 0.8785 (pm20) REVERT: B 145 ILE cc_start: 0.9562 (tp) cc_final: 0.9324 (tp) REVERT: B 150 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8785 (tp40) REVERT: B 167 LEU cc_start: 0.8921 (mt) cc_final: 0.8624 (mt) REVERT: B 174 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8231 (tp30) REVERT: B 186 ILE cc_start: 0.9619 (mt) cc_final: 0.9389 (mt) REVERT: B 190 MET cc_start: 0.9363 (mtm) cc_final: 0.9088 (mtm) REVERT: B 227 MET cc_start: 0.9230 (ptp) cc_final: 0.8653 (ptp) REVERT: B 314 MET cc_start: 0.8611 (ttt) cc_final: 0.7645 (tmm) REVERT: B 315 ASP cc_start: 0.8496 (p0) cc_final: 0.8239 (p0) REVERT: B 317 MET cc_start: 0.8407 (mtt) cc_final: 0.8164 (mpp) REVERT: B 322 MET cc_start: 0.8364 (mmt) cc_final: 0.8041 (mmm) REVERT: B 348 MET cc_start: 0.8454 (tpt) cc_final: 0.7976 (tpt) REVERT: B 352 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6787 (mm-30) REVERT: B 370 ASN cc_start: 0.9419 (m-40) cc_final: 0.9065 (m110) REVERT: B 375 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8455 (mtpt) REVERT: B 399 GLU cc_start: 0.8928 (tp30) cc_final: 0.8406 (tp30) REVERT: B 403 ILE cc_start: 0.9064 (mm) cc_final: 0.8839 (mm) REVERT: B 475 ASN cc_start: 0.9180 (m-40) cc_final: 0.8836 (m110) REVERT: B 498 TYR cc_start: 0.9148 (m-10) cc_final: 0.8941 (m-10) REVERT: B 501 GLN cc_start: 0.9559 (tt0) cc_final: 0.9250 (tt0) REVERT: B 550 MET cc_start: 0.8349 (mmt) cc_final: 0.8106 (mmt) REVERT: B 570 MET cc_start: 0.8913 (tpp) cc_final: 0.8502 (tpp) REVERT: B 599 GLU cc_start: 0.8258 (pt0) cc_final: 0.7845 (pt0) REVERT: B 624 PHE cc_start: 0.8829 (m-80) cc_final: 0.8552 (m-80) REVERT: B 640 MET cc_start: 0.8988 (tpp) cc_final: 0.8768 (tpp) REVERT: B 645 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8781 (tp-100) REVERT: C 130 TYR cc_start: 0.9027 (m-80) cc_final: 0.8679 (m-80) REVERT: C 157 MET cc_start: 0.8477 (mtm) cc_final: 0.8110 (mtm) REVERT: C 177 TYR cc_start: 0.8786 (t80) cc_final: 0.8550 (t80) REVERT: C 212 ILE cc_start: 0.6307 (mt) cc_final: 0.5879 (mt) REVERT: D 82 ASP cc_start: 0.8986 (m-30) cc_final: 0.8410 (p0) REVERT: D 117 THR cc_start: 0.9376 (p) cc_final: 0.8858 (p) REVERT: D 137 MET cc_start: 0.6685 (ttt) cc_final: 0.6337 (ppp) REVERT: D 230 ASP cc_start: 0.8940 (t70) cc_final: 0.8359 (m-30) REVERT: D 242 TYR cc_start: 0.9058 (t80) cc_final: 0.8702 (t80) REVERT: D 262 TYR cc_start: 0.8623 (t80) cc_final: 0.8384 (t80) REVERT: E 25 TRP cc_start: 0.8303 (p-90) cc_final: 0.7083 (p-90) outliers start: 1 outliers final: 0 residues processed: 613 average time/residue: 0.2814 time to fit residues: 258.1397 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 : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 17 optimal weight: 0.0980 chunk 77 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN C 69 GLN D 28 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.150665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105655 restraints weight = 45322.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109699 restraints weight = 27609.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112366 restraints weight = 18525.728| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 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 = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17041 Z= 0.146 Angle : 0.648 10.120 23026 Z= 0.334 Chirality : 0.044 0.191 2464 Planarity : 0.004 0.087 2931 Dihedral : 9.979 147.557 2325 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2012 helix: 1.05 (0.15), residues: 1150 sheet: -0.50 (0.38), residues: 189 loop : 0.08 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 623 HIS 0.011 0.001 HIS C 201 PHE 0.022 0.002 PHE B 129 TYR 0.021 0.002 TYR A 574 ARG 0.032 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 912) hydrogen bonds : angle 4.94042 ( 2664) SS BOND : bond 0.00562 ( 3) SS BOND : angle 4.03691 ( 6) covalent geometry : bond 0.00327 (17038) covalent geometry : angle 0.64507 (23020) *********************** 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 589 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8116 (ttp80) REVERT: A 190 MET cc_start: 0.9336 (mtm) cc_final: 0.8965 (mtm) REVERT: A 250 TYR cc_start: 0.7210 (m-80) cc_final: 0.6765 (m-80) REVERT: A 257 ASP cc_start: 0.8533 (m-30) cc_final: 0.8075 (m-30) REVERT: A 263 ASP cc_start: 0.8965 (m-30) cc_final: 0.8714 (m-30) REVERT: A 290 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8823 (tm-30) REVERT: A 291 LEU cc_start: 0.9686 (mt) cc_final: 0.9277 (mt) REVERT: A 301 PHE cc_start: 0.8717 (m-80) cc_final: 0.8360 (m-80) REVERT: A 312 GLN cc_start: 0.8461 (tp-100) cc_final: 0.7985 (tp40) REVERT: A 316 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 322 MET cc_start: 0.8820 (mmm) cc_final: 0.8558 (mmm) REVERT: A 362 ASP cc_start: 0.8352 (m-30) cc_final: 0.7999 (m-30) REVERT: A 390 GLN cc_start: 0.8496 (mm110) cc_final: 0.8254 (mm110) REVERT: A 393 SER cc_start: 0.9179 (t) cc_final: 0.8236 (t) REVERT: A 402 GLU cc_start: 0.8280 (mp0) cc_final: 0.7589 (mp0) REVERT: A 447 ASN cc_start: 0.8850 (m-40) cc_final: 0.8633 (m-40) REVERT: A 456 LYS cc_start: 0.9318 (ptpp) cc_final: 0.9090 (mtmm) REVERT: A 467 ASN cc_start: 0.9006 (t0) cc_final: 0.8354 (t0) REVERT: A 501 GLN cc_start: 0.9478 (tt0) cc_final: 0.9107 (tm-30) REVERT: A 586 TYR cc_start: 0.9131 (m-80) cc_final: 0.8557 (m-80) REVERT: A 590 SER cc_start: 0.8755 (t) cc_final: 0.7412 (p) REVERT: A 615 MET cc_start: 0.8993 (mmp) cc_final: 0.8648 (mmp) REVERT: A 628 GLU cc_start: 0.9367 (tt0) cc_final: 0.8975 (tp30) REVERT: A 650 GLN cc_start: 0.8517 (mt0) cc_final: 0.7804 (mt0) REVERT: A 664 THR cc_start: 0.9458 (p) cc_final: 0.9110 (p) REVERT: A 686 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7787 (mmm160) REVERT: B 40 TYR cc_start: 0.9226 (t80) cc_final: 0.8947 (t80) REVERT: B 95 MET cc_start: 0.8891 (tpp) cc_final: 0.8452 (tpp) REVERT: B 99 LYS cc_start: 0.9401 (tptm) cc_final: 0.9054 (tptp) REVERT: B 129 PHE cc_start: 0.9399 (m-80) cc_final: 0.8971 (m-80) REVERT: B 139 GLU cc_start: 0.9026 (pm20) cc_final: 0.8800 (pm20) REVERT: B 150 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8838 (tp40) REVERT: B 167 LEU cc_start: 0.8843 (mt) cc_final: 0.8604 (mt) REVERT: B 174 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8244 (tp30) REVERT: B 227 MET cc_start: 0.9163 (ptp) cc_final: 0.8597 (ptp) REVERT: B 314 MET cc_start: 0.8515 (ttt) cc_final: 0.7456 (tmm) REVERT: B 317 MET cc_start: 0.8420 (mtt) cc_final: 0.8178 (mpp) REVERT: B 322 MET cc_start: 0.8331 (mmt) cc_final: 0.8027 (mmm) REVERT: B 344 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 370 ASN cc_start: 0.9437 (m-40) cc_final: 0.9048 (m110) REVERT: B 375 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8476 (mtpt) REVERT: B 399 GLU cc_start: 0.8943 (tp30) cc_final: 0.8474 (tp30) REVERT: B 456 LYS cc_start: 0.9162 (pptt) cc_final: 0.8952 (mmmt) REVERT: B 475 ASN cc_start: 0.9374 (m-40) cc_final: 0.9109 (m110) REVERT: B 501 GLN cc_start: 0.9533 (tt0) cc_final: 0.9316 (tt0) REVERT: B 570 MET cc_start: 0.8967 (tpp) cc_final: 0.8361 (tpp) REVERT: B 624 PHE cc_start: 0.8807 (m-80) cc_final: 0.8539 (m-80) REVERT: B 640 MET cc_start: 0.8994 (tpp) cc_final: 0.8778 (tpp) REVERT: B 645 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8711 (tp-100) REVERT: B 656 LEU cc_start: 0.9309 (mt) cc_final: 0.9107 (mt) REVERT: B 657 PHE cc_start: 0.8846 (m-80) cc_final: 0.8213 (m-10) REVERT: C 157 MET cc_start: 0.8434 (mtm) cc_final: 0.8053 (mtm) REVERT: C 177 TYR cc_start: 0.8776 (t80) cc_final: 0.8542 (t80) REVERT: D 82 ASP cc_start: 0.8984 (m-30) cc_final: 0.8419 (p0) REVERT: D 137 MET cc_start: 0.6735 (ttt) cc_final: 0.6478 (ppp) REVERT: D 230 ASP cc_start: 0.8901 (t70) cc_final: 0.8306 (m-30) REVERT: D 242 TYR cc_start: 0.9050 (t80) cc_final: 0.8559 (t80) REVERT: D 262 TYR cc_start: 0.8688 (t80) cc_final: 0.8447 (t80) REVERT: E 25 TRP cc_start: 0.8372 (p-90) cc_final: 0.7741 (p-90) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.2819 time to fit residues: 249.1067 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 : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 147 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 390 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN D 186 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105513 restraints weight = 45566.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109740 restraints weight = 27536.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112258 restraints weight = 18544.480| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 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 = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17041 Z= 0.147 Angle : 0.653 8.640 23026 Z= 0.336 Chirality : 0.044 0.206 2464 Planarity : 0.004 0.061 2931 Dihedral : 9.793 147.748 2325 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2012 helix: 1.01 (0.15), residues: 1150 sheet: -0.56 (0.38), residues: 183 loop : 0.09 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 558 HIS 0.009 0.001 HIS C 201 PHE 0.028 0.002 PHE B 74 TYR 0.020 0.002 TYR B 118 ARG 0.016 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 912) hydrogen bonds : angle 4.97610 ( 2664) SS BOND : bond 0.00751 ( 3) SS BOND : angle 4.41377 ( 6) covalent geometry : bond 0.00325 (17038) covalent geometry : angle 0.64905 (23020) *********************** 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 597 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8905 (tpt) cc_final: 0.8365 (mmt) REVERT: A 164 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8099 (ttp80) REVERT: A 190 MET cc_start: 0.9318 (mtm) cc_final: 0.8939 (mtm) REVERT: A 250 TYR cc_start: 0.7249 (m-80) cc_final: 0.6821 (m-80) REVERT: A 257 ASP cc_start: 0.8509 (m-30) cc_final: 0.7964 (m-30) REVERT: A 263 ASP cc_start: 0.8992 (m-30) cc_final: 0.8772 (m-30) REVERT: A 290 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 291 LEU cc_start: 0.9703 (mt) cc_final: 0.9233 (mt) REVERT: A 301 PHE cc_start: 0.8636 (m-80) cc_final: 0.8357 (m-80) REVERT: A 312 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8001 (tp-100) REVERT: A 316 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 317 MET cc_start: 0.8771 (mmm) cc_final: 0.8506 (mmm) REVERT: A 322 MET cc_start: 0.8886 (mmm) cc_final: 0.8639 (mmm) REVERT: A 375 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8539 (mmtm) REVERT: A 447 ASN cc_start: 0.8836 (m-40) cc_final: 0.8589 (m-40) REVERT: A 456 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9078 (mtmm) REVERT: A 467 ASN cc_start: 0.9010 (t0) cc_final: 0.8690 (t0) REVERT: A 479 TYR cc_start: 0.8376 (t80) cc_final: 0.8005 (t80) REVERT: A 494 MET cc_start: 0.8490 (mmt) cc_final: 0.7982 (mmt) REVERT: A 501 GLN cc_start: 0.9464 (tt0) cc_final: 0.9098 (tm-30) REVERT: A 586 TYR cc_start: 0.9148 (m-80) cc_final: 0.8717 (m-80) REVERT: A 615 MET cc_start: 0.8997 (mmp) cc_final: 0.8651 (mmp) REVERT: A 632 MET cc_start: 0.8132 (mtp) cc_final: 0.7623 (mtp) REVERT: A 650 GLN cc_start: 0.8606 (mt0) cc_final: 0.8274 (mt0) REVERT: A 686 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7665 (mmm160) REVERT: B 40 TYR cc_start: 0.9208 (t80) cc_final: 0.8943 (t80) REVERT: B 52 LYS cc_start: 0.9430 (tptt) cc_final: 0.9186 (tppt) REVERT: B 55 LEU cc_start: 0.9502 (pp) cc_final: 0.9251 (pp) REVERT: B 95 MET cc_start: 0.8915 (tpp) cc_final: 0.8522 (tpp) REVERT: B 98 PHE cc_start: 0.9263 (t80) cc_final: 0.9041 (t80) REVERT: B 106 LEU cc_start: 0.9050 (tp) cc_final: 0.8533 (tp) REVERT: B 116 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8655 (mt-10) REVERT: B 129 PHE cc_start: 0.9393 (m-80) cc_final: 0.8964 (m-80) REVERT: B 167 LEU cc_start: 0.8919 (mt) cc_final: 0.8621 (mt) REVERT: B 174 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8327 (tp30) REVERT: B 227 MET cc_start: 0.9193 (ptp) cc_final: 0.8670 (ptp) REVERT: B 317 MET cc_start: 0.8321 (mtt) cc_final: 0.8119 (mpp) REVERT: B 322 MET cc_start: 0.8393 (mmt) cc_final: 0.8093 (mmm) REVERT: B 344 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 348 MET cc_start: 0.8515 (tpt) cc_final: 0.8116 (tpp) REVERT: B 352 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 370 ASN cc_start: 0.9427 (m-40) cc_final: 0.8994 (m110) REVERT: B 375 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8508 (mtpt) REVERT: B 403 ILE cc_start: 0.9107 (mm) cc_final: 0.8890 (mm) REVERT: B 415 ASN cc_start: 0.8869 (t0) cc_final: 0.8662 (t0) REVERT: B 426 GLU cc_start: 0.8992 (tp30) cc_final: 0.8752 (tp30) REVERT: B 456 LYS cc_start: 0.9175 (pptt) cc_final: 0.8952 (mmmt) REVERT: B 471 TYR cc_start: 0.9180 (t80) cc_final: 0.8907 (t80) REVERT: B 475 ASN cc_start: 0.9114 (m-40) cc_final: 0.8869 (m-40) REVERT: B 501 GLN cc_start: 0.9526 (tt0) cc_final: 0.9249 (tt0) REVERT: B 570 MET cc_start: 0.9143 (tpp) cc_final: 0.8597 (tpp) REVERT: B 604 ARG cc_start: 0.9176 (mmp80) cc_final: 0.8648 (mmp80) REVERT: B 624 PHE cc_start: 0.8883 (m-80) cc_final: 0.8591 (m-80) REVERT: B 645 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8719 (tp-100) REVERT: C 157 MET cc_start: 0.8383 (mtm) cc_final: 0.8002 (mtm) REVERT: C 177 TYR cc_start: 0.8825 (t80) cc_final: 0.8596 (t80) REVERT: D 16 ASP cc_start: 0.4074 (m-30) cc_final: 0.3770 (m-30) REVERT: D 74 MET cc_start: 0.5351 (tmm) cc_final: 0.5009 (tmm) REVERT: D 82 ASP cc_start: 0.8935 (m-30) cc_final: 0.8388 (p0) REVERT: D 116 GLU cc_start: 0.9434 (pm20) cc_final: 0.9055 (tm-30) REVERT: D 137 MET cc_start: 0.6806 (ttt) cc_final: 0.6454 (tmm) REVERT: D 230 ASP cc_start: 0.8978 (t70) cc_final: 0.8404 (m-30) REVERT: D 242 TYR cc_start: 0.9059 (t80) cc_final: 0.8528 (t80) REVERT: D 262 TYR cc_start: 0.8837 (t80) cc_final: 0.8598 (t80) REVERT: E 25 TRP cc_start: 0.8234 (p-90) cc_final: 0.7030 (p-90) outliers start: 0 outliers final: 0 residues processed: 597 average time/residue: 0.2834 time to fit residues: 254.4133 Evaluate side-chains 503 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103424 restraints weight = 45669.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107535 restraints weight = 27688.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110292 restraints weight = 18539.645| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17041 Z= 0.173 Angle : 0.671 10.419 23026 Z= 0.348 Chirality : 0.044 0.217 2464 Planarity : 0.004 0.060 2931 Dihedral : 9.732 152.133 2325 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2012 helix: 0.92 (0.15), residues: 1165 sheet: -0.69 (0.38), residues: 185 loop : 0.02 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 30 HIS 0.006 0.001 HIS D 201 PHE 0.030 0.002 PHE A 654 TYR 0.017 0.002 TYR A 574 ARG 0.012 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 912) hydrogen bonds : angle 5.04099 ( 2664) SS BOND : bond 0.00801 ( 3) SS BOND : angle 4.63049 ( 6) covalent geometry : bond 0.00382 (17038) covalent geometry : angle 0.66679 (23020) *********************** 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 594 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.9434 (t80) cc_final: 0.9176 (t80) REVERT: A 95 MET cc_start: 0.8837 (tpt) cc_final: 0.8308 (mmt) REVERT: A 139 GLU cc_start: 0.9015 (mp0) cc_final: 0.8741 (mp0) REVERT: A 164 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8022 (ttp80) REVERT: A 186 ILE cc_start: 0.9531 (mm) cc_final: 0.9300 (mm) REVERT: A 190 MET cc_start: 0.9284 (mtm) cc_final: 0.8976 (mtm) REVERT: A 250 TYR cc_start: 0.7228 (m-80) cc_final: 0.6826 (m-80) REVERT: A 257 ASP cc_start: 0.8536 (m-30) cc_final: 0.8142 (m-30) REVERT: A 263 ASP cc_start: 0.8937 (m-30) cc_final: 0.8641 (m-30) REVERT: A 290 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 291 LEU cc_start: 0.9698 (mt) cc_final: 0.9218 (mt) REVERT: A 301 PHE cc_start: 0.8651 (m-80) cc_final: 0.8332 (m-80) REVERT: A 312 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8020 (tp-100) REVERT: A 316 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 319 MET cc_start: 0.8907 (tpt) cc_final: 0.8677 (tpp) REVERT: A 447 ASN cc_start: 0.8815 (m-40) cc_final: 0.8576 (m-40) REVERT: A 467 ASN cc_start: 0.9079 (t0) cc_final: 0.8812 (t0) REVERT: A 490 THR cc_start: 0.8939 (m) cc_final: 0.7700 (p) REVERT: A 493 MET cc_start: 0.8101 (ttm) cc_final: 0.7804 (mtm) REVERT: A 494 MET cc_start: 0.8511 (mmt) cc_final: 0.7983 (mmt) REVERT: A 501 GLN cc_start: 0.9466 (tt0) cc_final: 0.9090 (tm-30) REVERT: A 586 TYR cc_start: 0.9118 (m-80) cc_final: 0.8854 (m-80) REVERT: A 632 MET cc_start: 0.8027 (mtp) cc_final: 0.7661 (mtp) REVERT: A 662 MET cc_start: 0.9024 (pmm) cc_final: 0.8608 (pmm) REVERT: A 664 THR cc_start: 0.9454 (p) cc_final: 0.9102 (p) REVERT: A 668 ASN cc_start: 0.9069 (m-40) cc_final: 0.8868 (m-40) REVERT: A 686 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7654 (mmm160) REVERT: B 18 ILE cc_start: 0.9282 (mm) cc_final: 0.8951 (mm) REVERT: B 40 TYR cc_start: 0.9205 (t80) cc_final: 0.8955 (t80) REVERT: B 52 LYS cc_start: 0.9454 (tptt) cc_final: 0.9228 (tppt) REVERT: B 55 LEU cc_start: 0.9502 (pp) cc_final: 0.9225 (pp) REVERT: B 95 MET cc_start: 0.8913 (tpp) cc_final: 0.8560 (tpp) REVERT: B 117 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7374 (mtp85) REVERT: B 120 ASP cc_start: 0.9516 (m-30) cc_final: 0.9218 (m-30) REVERT: B 129 PHE cc_start: 0.9392 (m-80) cc_final: 0.8984 (m-80) REVERT: B 167 LEU cc_start: 0.8947 (mt) cc_final: 0.8672 (mt) REVERT: B 174 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8430 (tp30) REVERT: B 227 MET cc_start: 0.9170 (ptp) cc_final: 0.8611 (ptp) REVERT: B 235 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: B 312 GLN cc_start: 0.8625 (tt0) cc_final: 0.8419 (tt0) REVERT: B 314 MET cc_start: 0.8653 (ttp) cc_final: 0.8165 (tmm) REVERT: B 322 MET cc_start: 0.8390 (mmt) cc_final: 0.8060 (mmm) REVERT: B 344 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8276 (mt-10) REVERT: B 348 MET cc_start: 0.8454 (tpt) cc_final: 0.7842 (tpp) REVERT: B 352 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6623 (mm-30) REVERT: B 370 ASN cc_start: 0.9415 (m-40) cc_final: 0.8979 (m110) REVERT: B 375 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8478 (mtpt) REVERT: B 390 GLN cc_start: 0.9247 (mt0) cc_final: 0.9016 (mm-40) REVERT: B 403 ILE cc_start: 0.9107 (mm) cc_final: 0.8896 (mm) REVERT: B 426 GLU cc_start: 0.9018 (tp30) cc_final: 0.8684 (tp30) REVERT: B 475 ASN cc_start: 0.9184 (m-40) cc_final: 0.8832 (m110) REVERT: B 483 GLU cc_start: 0.9329 (pm20) cc_final: 0.9089 (pm20) REVERT: B 501 GLN cc_start: 0.9476 (tt0) cc_final: 0.9213 (tt0) REVERT: B 516 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8586 (tp-100) REVERT: B 570 MET cc_start: 0.9201 (tpp) cc_final: 0.8676 (tpp) REVERT: B 598 MET cc_start: 0.8587 (ttm) cc_final: 0.8362 (ttm) REVERT: B 624 PHE cc_start: 0.8779 (m-80) cc_final: 0.8573 (m-80) REVERT: B 645 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8790 (tp-100) REVERT: B 650 GLN cc_start: 0.7013 (mt0) cc_final: 0.6224 (mt0) REVERT: C 157 MET cc_start: 0.8353 (mtm) cc_final: 0.7954 (mtm) REVERT: D 16 ASP cc_start: 0.4909 (m-30) cc_final: 0.4498 (m-30) REVERT: D 74 MET cc_start: 0.5434 (tmm) cc_final: 0.5132 (tmm) REVERT: D 82 ASP cc_start: 0.8939 (m-30) cc_final: 0.8437 (p0) REVERT: D 116 GLU cc_start: 0.9358 (pm20) cc_final: 0.9048 (tm-30) REVERT: D 117 THR cc_start: 0.9356 (p) cc_final: 0.9119 (p) REVERT: D 137 MET cc_start: 0.6790 (ttt) cc_final: 0.6540 (ppp) REVERT: D 230 ASP cc_start: 0.8955 (t70) cc_final: 0.8358 (m-30) REVERT: D 262 TYR cc_start: 0.8839 (t80) cc_final: 0.8599 (t80) REVERT: E 34 MET cc_start: 0.8970 (ptt) cc_final: 0.8715 (ppp) REVERT: E 97 GLN cc_start: 0.8926 (mt0) cc_final: 0.8717 (mp10) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.2766 time to fit residues: 247.1953 Evaluate side-chains 500 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 390 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105911 restraints weight = 46352.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109868 restraints weight = 28753.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112264 restraints weight = 19605.648| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17041 Z= 0.160 Angle : 0.685 11.039 23026 Z= 0.356 Chirality : 0.045 0.192 2464 Planarity : 0.004 0.054 2931 Dihedral : 9.678 150.409 2325 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2012 helix: 0.92 (0.15), residues: 1162 sheet: -0.64 (0.38), residues: 191 loop : -0.08 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 558 HIS 0.007 0.001 HIS D 201 PHE 0.023 0.002 PHE C 92 TYR 0.027 0.002 TYR B 471 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 912) hydrogen bonds : angle 5.10305 ( 2664) SS BOND : bond 0.00491 ( 3) SS BOND : angle 4.56131 ( 6) covalent geometry : bond 0.00360 (17038) covalent geometry : angle 0.68126 (23020) *********************** 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 576 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9701 (mm) cc_final: 0.9447 (pp) REVERT: A 95 MET cc_start: 0.8907 (tpt) cc_final: 0.8486 (mmt) REVERT: A 147 GLN cc_start: 0.9167 (tt0) cc_final: 0.8906 (tt0) REVERT: A 161 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7500 (ptp-110) REVERT: A 164 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8147 (ttp80) REVERT: A 186 ILE cc_start: 0.9512 (mm) cc_final: 0.9282 (mm) REVERT: A 190 MET cc_start: 0.9285 (mtm) cc_final: 0.8971 (mtm) REVERT: A 250 TYR cc_start: 0.7261 (m-80) cc_final: 0.6893 (m-80) REVERT: A 257 ASP cc_start: 0.8629 (m-30) cc_final: 0.8002 (m-30) REVERT: A 263 ASP cc_start: 0.8985 (m-30) cc_final: 0.8720 (m-30) REVERT: A 290 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 291 LEU cc_start: 0.9681 (mt) cc_final: 0.9262 (mt) REVERT: A 301 PHE cc_start: 0.8654 (m-80) cc_final: 0.8354 (m-80) REVERT: A 312 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8102 (tp-100) REVERT: A 316 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 317 MET cc_start: 0.8786 (mmm) cc_final: 0.8482 (mmm) REVERT: A 322 MET cc_start: 0.8914 (mmm) cc_final: 0.8654 (mmm) REVERT: A 447 ASN cc_start: 0.8795 (m-40) cc_final: 0.8573 (m-40) REVERT: A 467 ASN cc_start: 0.9112 (t0) cc_final: 0.8753 (t0) REVERT: A 490 THR cc_start: 0.8985 (m) cc_final: 0.7755 (p) REVERT: A 493 MET cc_start: 0.8071 (ttm) cc_final: 0.7752 (mtm) REVERT: A 494 MET cc_start: 0.8499 (mmt) cc_final: 0.8012 (mmt) REVERT: A 501 GLN cc_start: 0.9463 (tt0) cc_final: 0.9087 (tm-30) REVERT: A 586 TYR cc_start: 0.9123 (m-80) cc_final: 0.8912 (m-80) REVERT: A 615 MET cc_start: 0.8777 (mmp) cc_final: 0.8405 (mmp) REVERT: A 664 THR cc_start: 0.9485 (p) cc_final: 0.9155 (p) REVERT: A 686 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7630 (mmm160) REVERT: B 40 TYR cc_start: 0.9191 (t80) cc_final: 0.8885 (t80) REVERT: B 52 LYS cc_start: 0.9445 (tptt) cc_final: 0.9219 (tppt) REVERT: B 55 LEU cc_start: 0.9505 (pp) cc_final: 0.9226 (pp) REVERT: B 95 MET cc_start: 0.8880 (tpp) cc_final: 0.8605 (tpp) REVERT: B 117 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7277 (mtp85) REVERT: B 120 ASP cc_start: 0.9499 (m-30) cc_final: 0.9194 (m-30) REVERT: B 129 PHE cc_start: 0.9436 (m-80) cc_final: 0.9001 (m-80) REVERT: B 167 LEU cc_start: 0.8931 (mt) cc_final: 0.8650 (mt) REVERT: B 174 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8405 (tp30) REVERT: B 184 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8706 (ttp-170) REVERT: B 227 MET cc_start: 0.9174 (ptp) cc_final: 0.8615 (ptp) REVERT: B 235 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8100 (mtm-85) REVERT: B 257 ASP cc_start: 0.8852 (m-30) cc_final: 0.7842 (m-30) REVERT: B 314 MET cc_start: 0.8638 (ttp) cc_final: 0.7641 (tmm) REVERT: B 322 MET cc_start: 0.8397 (mmt) cc_final: 0.8142 (mmm) REVERT: B 344 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 348 MET cc_start: 0.8479 (tpt) cc_final: 0.7893 (tpp) REVERT: B 352 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 370 ASN cc_start: 0.9410 (m-40) cc_final: 0.8976 (m110) REVERT: B 375 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8472 (mtpt) REVERT: B 426 GLU cc_start: 0.8996 (tp30) cc_final: 0.8681 (tp30) REVERT: B 447 ASN cc_start: 0.8571 (m110) cc_final: 0.8315 (m110) REVERT: B 501 GLN cc_start: 0.9472 (tt0) cc_final: 0.9210 (tt0) REVERT: B 570 MET cc_start: 0.9207 (tpp) cc_final: 0.8674 (tpp) REVERT: B 602 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 624 PHE cc_start: 0.9002 (m-80) cc_final: 0.8645 (m-80) REVERT: B 627 LYS cc_start: 0.9266 (pttp) cc_final: 0.8902 (ptmt) REVERT: B 632 MET cc_start: 0.8460 (mpp) cc_final: 0.8205 (mpp) REVERT: B 645 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8901 (tp-100) REVERT: C 157 MET cc_start: 0.8262 (mtm) cc_final: 0.7865 (mtm) REVERT: D 74 MET cc_start: 0.5580 (tmm) cc_final: 0.5218 (tmm) REVERT: D 82 ASP cc_start: 0.8976 (m-30) cc_final: 0.8504 (p0) REVERT: D 116 GLU cc_start: 0.9423 (pm20) cc_final: 0.8944 (tm-30) REVERT: D 117 THR cc_start: 0.9337 (p) cc_final: 0.8983 (p) REVERT: D 137 MET cc_start: 0.6719 (ttt) cc_final: 0.6519 (ppp) REVERT: D 230 ASP cc_start: 0.8926 (t70) cc_final: 0.8331 (m-30) REVERT: D 242 TYR cc_start: 0.9125 (t80) cc_final: 0.8616 (t80) REVERT: D 262 TYR cc_start: 0.8908 (t80) cc_final: 0.8664 (t80) REVERT: E 25 TRP cc_start: 0.8309 (p-90) cc_final: 0.7114 (p-90) REVERT: E 34 MET cc_start: 0.8960 (ptt) cc_final: 0.8673 (ppp) REVERT: E 93 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6656 (mmmt) REVERT: E 97 GLN cc_start: 0.8888 (mt0) cc_final: 0.8661 (mp10) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.2920 time to fit residues: 252.5600 Evaluate side-chains 501 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 312 GLN A 390 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** B 142 ASN ** 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 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104545 restraints weight = 46040.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108694 restraints weight = 28089.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111418 restraints weight = 19099.993| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 17041 Z= 0.170 Angle : 0.704 12.217 23026 Z= 0.366 Chirality : 0.046 0.232 2464 Planarity : 0.004 0.054 2931 Dihedral : 9.656 151.781 2325 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2012 helix: 0.86 (0.15), residues: 1159 sheet: -0.81 (0.37), residues: 195 loop : -0.13 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 30 HIS 0.008 0.001 HIS C 201 PHE 0.025 0.002 PHE C 92 TYR 0.020 0.002 TYR B 471 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 912) hydrogen bonds : angle 5.21293 ( 2664) SS BOND : bond 0.00595 ( 3) SS BOND : angle 5.38285 ( 6) covalent geometry : bond 0.00382 (17038) covalent geometry : angle 0.69858 (23020) ********************** 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 584 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 2.298 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 55 LEU cc_start: 0.9691 (mm) cc_final: 0.9459 (pp) REVERT: A 95 MET cc_start: 0.8876 (tpt) cc_final: 0.8351 (mmt) REVERT: A 161 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7526 (ptp-110) REVERT: A 164 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8184 (ttp80) REVERT: A 186 ILE cc_start: 0.9508 (mm) cc_final: 0.9295 (mm) REVERT: A 190 MET cc_start: 0.9349 (mtm) cc_final: 0.9033 (mtm) REVERT: A 250 TYR cc_start: 0.7346 (m-80) cc_final: 0.6957 (m-80) REVERT: A 257 ASP cc_start: 0.8469 (m-30) cc_final: 0.8086 (m-30) REVERT: A 263 ASP cc_start: 0.9030 (m-30) cc_final: 0.8741 (m-30) REVERT: A 290 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 291 LEU cc_start: 0.9693 (mt) cc_final: 0.9272 (mt) REVERT: A 301 PHE cc_start: 0.8683 (m-80) cc_final: 0.8350 (m-80) REVERT: A 312 GLN cc_start: 0.8388 (tp40) cc_final: 0.8006 (tp-100) REVERT: A 316 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 317 MET cc_start: 0.8741 (mmm) cc_final: 0.8452 (mmm) REVERT: A 366 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8833 (ptpp) REVERT: A 447 ASN cc_start: 0.8856 (m-40) cc_final: 0.8639 (m-40) REVERT: A 467 ASN cc_start: 0.9103 (t0) cc_final: 0.8499 (t0) REVERT: A 479 TYR cc_start: 0.8249 (t80) cc_final: 0.7612 (t80) REVERT: A 490 THR cc_start: 0.8914 (m) cc_final: 0.7754 (p) REVERT: A 493 MET cc_start: 0.7975 (ttm) cc_final: 0.7693 (mtm) REVERT: A 494 MET cc_start: 0.8465 (mmt) cc_final: 0.7989 (mmt) REVERT: A 501 GLN cc_start: 0.9464 (tt0) cc_final: 0.9065 (tm-30) REVERT: A 590 SER cc_start: 0.8784 (t) cc_final: 0.7953 (p) REVERT: A 591 THR cc_start: 0.8383 (t) cc_final: 0.8150 (t) REVERT: A 615 MET cc_start: 0.8799 (mmp) cc_final: 0.8390 (mmp) REVERT: A 628 GLU cc_start: 0.9414 (tt0) cc_final: 0.8947 (mm-30) REVERT: A 686 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7721 (mmm160) REVERT: B 18 ILE cc_start: 0.9304 (mm) cc_final: 0.8935 (mm) REVERT: B 95 MET cc_start: 0.8890 (tpp) cc_final: 0.8623 (tpp) REVERT: B 99 LYS cc_start: 0.9519 (tptm) cc_final: 0.9117 (tptp) REVERT: B 117 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7328 (mtp85) REVERT: B 120 ASP cc_start: 0.9483 (m-30) cc_final: 0.9201 (m-30) REVERT: B 129 PHE cc_start: 0.9455 (m-80) cc_final: 0.8944 (m-80) REVERT: B 167 LEU cc_start: 0.8955 (mt) cc_final: 0.8667 (mt) REVERT: B 174 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8308 (tp30) REVERT: B 227 MET cc_start: 0.9112 (ptp) cc_final: 0.8661 (ptp) REVERT: B 314 MET cc_start: 0.8753 (ttp) cc_final: 0.8385 (tmm) REVERT: B 322 MET cc_start: 0.8473 (mmt) cc_final: 0.8071 (mmm) REVERT: B 344 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 370 ASN cc_start: 0.9412 (m-40) cc_final: 0.8950 (m110) REVERT: B 375 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8471 (mtpt) REVERT: B 501 GLN cc_start: 0.9474 (tt0) cc_final: 0.9162 (tt0) REVERT: B 516 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8665 (tp-100) REVERT: B 570 MET cc_start: 0.9198 (tpp) cc_final: 0.8712 (tpp) REVERT: B 588 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8494 (mm-40) REVERT: B 624 PHE cc_start: 0.8967 (m-80) cc_final: 0.8703 (m-80) REVERT: B 627 LYS cc_start: 0.9306 (pttp) cc_final: 0.8891 (ptmt) REVERT: B 645 GLN cc_start: 0.9267 (tp-100) cc_final: 0.8999 (tp-100) REVERT: B 677 ARG cc_start: 0.8726 (mmm160) cc_final: 0.7963 (mmm160) REVERT: C 157 MET cc_start: 0.8327 (mtm) cc_final: 0.7948 (mtm) REVERT: D 74 MET cc_start: 0.5653 (tmm) cc_final: 0.5321 (tmm) REVERT: D 82 ASP cc_start: 0.8996 (m-30) cc_final: 0.8679 (p0) REVERT: D 116 GLU cc_start: 0.9434 (pm20) cc_final: 0.8939 (tm-30) REVERT: D 117 THR cc_start: 0.9340 (p) cc_final: 0.8985 (p) REVERT: D 230 ASP cc_start: 0.8960 (t70) cc_final: 0.8373 (m-30) REVERT: D 242 TYR cc_start: 0.9110 (t80) cc_final: 0.8591 (t80) REVERT: D 262 TYR cc_start: 0.8823 (t80) cc_final: 0.8557 (t80) REVERT: E 25 TRP cc_start: 0.8307 (p-90) cc_final: 0.7052 (p-90) REVERT: E 34 MET cc_start: 0.8964 (ptt) cc_final: 0.8651 (ppp) REVERT: E 97 GLN cc_start: 0.8897 (mt0) cc_final: 0.8671 (mp10) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 0.3220 time to fit residues: 288.1932 Evaluate side-chains 509 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 390 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** 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** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 136 GLN ** D 238 ASN ** 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 = 0.4020 r_free = 0.4020 target = 0.147738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103421 restraints weight = 46641.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107333 restraints weight = 29043.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109964 restraints weight = 19719.515| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17041 Z= 0.186 Angle : 0.712 12.697 23026 Z= 0.370 Chirality : 0.046 0.226 2464 Planarity : 0.004 0.053 2931 Dihedral : 9.680 152.408 2325 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2012 helix: 0.80 (0.15), residues: 1160 sheet: -0.64 (0.39), residues: 180 loop : -0.18 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 30 HIS 0.006 0.001 HIS C 201 PHE 0.025 0.002 PHE A 492 TYR 0.022 0.002 TYR B 498 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 912) hydrogen bonds : angle 5.23422 ( 2664) SS BOND : bond 0.00858 ( 3) SS BOND : angle 4.97752 ( 6) covalent geometry : bond 0.00411 (17038) covalent geometry : angle 0.70770 (23020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7826.57 seconds wall clock time: 138 minutes 49.77 seconds (8329.77 seconds total)