Starting phenix.real_space_refine on Sun May 18 04:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxx_45014/05_2025/9bxx_45014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxx_45014/05_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_45014/05_2025/9bxx_45014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxx_45014/05_2025/9bxx_45014.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxx_45014/05_2025/9bxx_45014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxx_45014/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.42, per 1000 atoms: 0.56 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: 4.43 Conformation dependent library (CDL) restraints added in 2.1 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: 1.94 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: 5.42 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5044 1.34 - 1.46: 3105 1.46 - 1.58: 8700 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17038 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.40e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.59e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.91e+00 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22240 2.09 - 4.19: 705 4.19 - 6.28: 64 6.28 - 8.37: 9 8.37 - 10.46: 2 Bond angle restraints: 23020 Sorted by residual: angle pdb=" C VAL E 69 " pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " ideal model delta sigma weight residual 111.15 119.33 -8.18 1.30e+00 5.92e-01 3.96e+01 angle pdb=" CA VAL E 69 " pdb=" CB VAL E 69 " pdb=" CG1 VAL E 69 " ideal model delta sigma weight residual 110.40 118.71 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.50 -4.31 1.06e+00 8.90e-01 1.65e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 9642 29.73 - 59.46: 547 59.46 - 89.19: 60 89.19 - 118.92: 3 118.92 - 148.65: 4 Dihedral angle restraints: 10256 sinusoidal: 4264 harmonic: 5992 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.28 84.28 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 153.03 148.65 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 156.37 145.31 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 10253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2223 0.093 - 0.186: 203 0.186 - 0.280: 33 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.078 2.00e-02 2.50e+03 3.70e-02 3.43e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.041 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP B 623 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 124 2.51 - 3.11: 12002 3.11 - 3.70: 27791 3.70 - 4.30: 42534 4.30 - 4.90: 68522 Nonbonded interactions: 150973 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.040 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- 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 : 1.861 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: 0.8240 (mm) REVERT: A 99 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8870 (mmmm) REVERT: A 147 GLN cc_start: 0.8226 (mt0) cc_final: 0.7781 (mt0) REVERT: A 181 ASP cc_start: 0.8683 (m-30) cc_final: 0.8360 (m-30) REVERT: A 188 ILE cc_start: 0.8849 (mt) cc_final: 0.8404 (mt) REVERT: A 257 ASP cc_start: 0.8033 (m-30) cc_final: 0.7791 (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: 0.7830 (tmm) REVERT: A 500 ILE cc_start: 0.9119 (mt) cc_final: 0.8768 (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: 0.8468 (mt) REVERT: A 594 VAL cc_start: 0.8429 (m) cc_final: 0.8179 (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: 0.8666 (mt) REVERT: B 68 PHE cc_start: 0.8403 (p90) cc_final: 0.7981 (p90) REVERT: B 69 LEU cc_start: 0.8205 (mt) cc_final: 0.7909 (mt) REVERT: B 87 LYS cc_start: 0.8400 (tptp) cc_final: 0.8117 (tptp) REVERT: B 172 LEU cc_start: 0.8956 (mp) cc_final: 0.8665 (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: 0.7412 (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: 0.8690 (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: 0.8347 (tp) REVERT: B 472 LEU cc_start: 0.8818 (mt) cc_final: 0.8456 (mt) REVERT: B 493 MET cc_start: 0.7793 (tmm) cc_final: 0.7566 (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: 0.7531 (m-80) REVERT: B 575 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7348 (mtm-85) REVERT: B 576 LEU cc_start: 0.8791 (mt) cc_final: 0.8409 (mt) REVERT: B 589 SER cc_start: 0.8776 (m) cc_final: 0.8322 (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: 0.8632 (mp) REVERT: B 664 THR cc_start: 0.8929 (p) cc_final: 0.8567 (t) REVERT: C 33 GLU cc_start: 0.1904 (mp0) cc_final: 0.1278 (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: 0.2523 (m170) REVERT: C 316 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6716 (mtmm) REVERT: D 63 THR cc_start: 0.5201 (m) cc_final: 0.4942 (m) REVERT: D 286 VAL cc_start: 0.3482 (t) cc_final: 0.2958 (p) REVERT: E 78 LEU cc_start: 0.6809 (mp) cc_final: 0.6310 (mp) outliers start: 25 outliers final: 3 residues processed: 874 average time/residue: 0.3269 time to fit residues: 416.0629 Evaluate side-chains 566 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 562 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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** A 588 GLN B 19 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110855 restraints weight = 42962.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114940 restraints weight = 26182.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117807 restraints weight = 17658.338| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17041 Z= 0.178 Angle : 0.662 13.778 23026 Z= 0.351 Chirality : 0.044 0.227 2464 Planarity : 0.004 0.048 2931 Dihedral : 10.628 158.645 2325 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.28 % Allowed : 2.96 % Favored : 96.76 % 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: 1.11 (0.18), residues: 2012 helix: 1.27 (0.15), residues: 1151 sheet: -0.44 (0.35), residues: 187 loop : 0.38 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.008 0.002 HIS D 80 PHE 0.028 0.002 PHE C 320 TYR 0.034 0.002 TYR B 36 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 912) hydrogen bonds : angle 5.15684 ( 2664) SS BOND : bond 0.00528 ( 3) SS BOND : angle 7.13101 ( 6) covalent geometry : bond 0.00387 (17038) covalent geometry : angle 0.65217 (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 676 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 671 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9290 (tppp) REVERT: A 142 ASN cc_start: 0.9303 (m-40) cc_final: 0.9005 (m110) REVERT: A 186 ILE cc_start: 0.9531 (mm) cc_final: 0.9306 (mm) REVERT: A 188 ILE cc_start: 0.9604 (mt) cc_final: 0.9260 (mt) REVERT: A 190 MET cc_start: 0.9293 (mtm) cc_final: 0.9006 (mtm) REVERT: A 250 TYR cc_start: 0.7132 (m-80) cc_final: 0.6655 (m-80) REVERT: A 257 ASP cc_start: 0.8650 (m-30) cc_final: 0.7971 (m-30) REVERT: A 263 ASP cc_start: 0.9003 (m-30) cc_final: 0.8570 (m-30) REVERT: A 286 ASP cc_start: 0.9069 (m-30) cc_final: 0.8826 (m-30) REVERT: A 291 LEU cc_start: 0.9441 (mt) cc_final: 0.9238 (mt) REVERT: A 301 PHE cc_start: 0.8819 (m-80) cc_final: 0.8179 (m-10) REVERT: A 312 GLN cc_start: 0.8694 (tp40) cc_final: 0.8493 (tp40) REVERT: A 342 LEU cc_start: 0.9641 (tp) cc_final: 0.9421 (tp) REVERT: A 361 GLN cc_start: 0.8825 (tt0) cc_final: 0.8364 (tp40) REVERT: A 362 ASP cc_start: 0.8306 (m-30) cc_final: 0.7912 (m-30) REVERT: A 466 MET cc_start: 0.8986 (ptt) cc_final: 0.8694 (ptt) REVERT: A 474 GLN cc_start: 0.8741 (mt0) cc_final: 0.8510 (mt0) REVERT: A 475 ASN cc_start: 0.8778 (m-40) cc_final: 0.8332 (m110) REVERT: A 501 GLN cc_start: 0.9387 (tt0) cc_final: 0.9015 (tm-30) REVERT: A 615 MET cc_start: 0.8429 (mmp) cc_final: 0.6770 (mmp) REVERT: A 630 TYR cc_start: 0.7085 (m-80) cc_final: 0.5099 (m-80) REVERT: A 645 GLN cc_start: 0.8478 (tp40) cc_final: 0.7789 (tp40) REVERT: A 664 THR cc_start: 0.9286 (p) cc_final: 0.8719 (p) REVERT: A 668 ASN cc_start: 0.8934 (m-40) cc_final: 0.8333 (m-40) REVERT: A 673 TYR cc_start: 0.9067 (t80) cc_final: 0.8508 (t80) REVERT: A 686 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7186 (mmm160) REVERT: B 18 ILE cc_start: 0.9238 (mm) cc_final: 0.9027 (pt) REVERT: B 23 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9041 (mmtm) REVERT: B 121 ARG cc_start: 0.9140 (tpm170) cc_final: 0.8924 (tpt170) REVERT: B 144 MET cc_start: 0.9298 (mtm) cc_final: 0.8360 (mtm) REVERT: B 145 ILE cc_start: 0.9431 (tp) cc_final: 0.9176 (tp) REVERT: B 172 LEU cc_start: 0.8811 (mp) cc_final: 0.8485 (mp) REVERT: B 179 LEU cc_start: 0.9610 (tp) cc_final: 0.9401 (tp) REVERT: B 184 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8273 (mtm180) REVERT: B 186 ILE cc_start: 0.9724 (mt) cc_final: 0.9495 (mt) REVERT: B 190 MET cc_start: 0.9386 (mtm) cc_final: 0.8939 (mtm) REVERT: B 250 TYR cc_start: 0.8255 (m-80) cc_final: 0.7942 (m-80) REVERT: B 296 LYS cc_start: 0.8780 (mmpt) cc_final: 0.8443 (tptt) REVERT: B 335 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 355 TYR cc_start: 0.8824 (m-80) cc_final: 0.8574 (m-10) REVERT: B 370 ASN cc_start: 0.9259 (m-40) cc_final: 0.9019 (m110) REVERT: B 375 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8123 (mmmm) REVERT: B 390 GLN cc_start: 0.9212 (mt0) cc_final: 0.8938 (mm-40) REVERT: B 403 ILE cc_start: 0.9246 (mm) cc_final: 0.8983 (mm) REVERT: B 477 ILE cc_start: 0.8490 (mm) cc_final: 0.8232 (mp) REVERT: B 493 MET cc_start: 0.9314 (tmm) cc_final: 0.9108 (tmm) REVERT: B 496 ASN cc_start: 0.9362 (t0) cc_final: 0.8741 (t0) REVERT: B 500 ILE cc_start: 0.9341 (mt) cc_final: 0.9015 (mt) REVERT: B 501 GLN cc_start: 0.9542 (tt0) cc_final: 0.9029 (pt0) REVERT: B 516 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8595 (tp40) REVERT: B 550 MET cc_start: 0.7683 (mtm) cc_final: 0.7328 (mtp) REVERT: B 586 TYR cc_start: 0.9473 (m-80) cc_final: 0.8968 (m-80) REVERT: B 604 ARG cc_start: 0.9285 (mmp80) cc_final: 0.9033 (mmp80) REVERT: B 626 TYR cc_start: 0.8317 (m-80) cc_final: 0.7915 (m-10) REVERT: B 640 MET cc_start: 0.9023 (tpp) cc_final: 0.8645 (tpp) REVERT: B 645 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8900 (tp-100) REVERT: B 664 THR cc_start: 0.8836 (p) cc_final: 0.8416 (t) REVERT: B 686 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8036 (mmm160) REVERT: C 33 GLU cc_start: 0.4416 (mp0) cc_final: 0.3773 (tm-30) REVERT: C 157 MET cc_start: 0.8573 (mtm) cc_final: 0.8095 (mtm) REVERT: C 177 TYR cc_start: 0.8963 (t80) cc_final: 0.8600 (t80) REVERT: D 82 ASP cc_start: 0.8805 (m-30) cc_final: 0.7998 (p0) REVERT: D 137 MET cc_start: 0.5743 (ttt) cc_final: 0.5113 (tmm) REVERT: D 227 PHE cc_start: 0.6979 (t80) cc_final: 0.6698 (t80) REVERT: D 230 ASP cc_start: 0.8973 (t70) cc_final: 0.8428 (m-30) REVERT: D 242 TYR cc_start: 0.8928 (t80) cc_final: 0.8540 (t80) REVERT: D 262 TYR cc_start: 0.8405 (t80) cc_final: 0.8159 (t80) REVERT: D 269 MET cc_start: -0.3142 (mmp) cc_final: -0.3380 (mmp) outliers start: 5 outliers final: 2 residues processed: 674 average time/residue: 0.2939 time to fit residues: 293.5003 Evaluate side-chains 536 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 534 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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: 0.6980 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110034 restraints weight = 43715.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114101 restraints weight = 26963.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116845 restraints weight = 18286.054| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17041 Z= 0.148 Angle : 0.610 8.235 23026 Z= 0.322 Chirality : 0.043 0.212 2464 Planarity : 0.004 0.090 2931 Dihedral : 10.456 157.406 2325 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.18), residues: 2012 helix: 1.35 (0.15), residues: 1143 sheet: 0.08 (0.41), residues: 153 loop : 0.23 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 558 HIS 0.018 0.001 HIS C 201 PHE 0.031 0.002 PHE A 492 TYR 0.031 0.002 TYR A 574 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 912) hydrogen bonds : angle 4.92007 ( 2664) SS BOND : bond 0.01887 ( 3) SS BOND : angle 3.39535 ( 6) covalent geometry : bond 0.00319 (17038) covalent geometry : angle 0.60803 (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 637 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 636 time to evaluate : 1.923 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 12 LEU cc_start: 0.9675 (mt) cc_final: 0.9443 (mt) REVERT: A 119 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8460 (mt-10) REVERT: A 147 GLN cc_start: 0.9004 (mt0) cc_final: 0.8344 (mt0) REVERT: A 186 ILE cc_start: 0.9535 (mm) cc_final: 0.9221 (mm) REVERT: A 188 ILE cc_start: 0.9540 (mt) cc_final: 0.9199 (mt) REVERT: A 190 MET cc_start: 0.9288 (mtm) cc_final: 0.8975 (mtm) REVERT: A 250 TYR cc_start: 0.7274 (m-80) cc_final: 0.6855 (m-80) REVERT: A 257 ASP cc_start: 0.8651 (m-30) cc_final: 0.8236 (m-30) REVERT: A 263 ASP cc_start: 0.9040 (m-30) cc_final: 0.8703 (m-30) REVERT: A 290 GLU cc_start: 0.9266 (tm-30) cc_final: 0.9005 (tm-30) REVERT: A 291 LEU cc_start: 0.9614 (mt) cc_final: 0.9233 (mt) REVERT: A 301 PHE cc_start: 0.8815 (m-80) cc_final: 0.8287 (m-80) REVERT: A 312 GLN cc_start: 0.8478 (tp40) cc_final: 0.8135 (tp40) REVERT: A 322 MET cc_start: 0.8913 (mmm) cc_final: 0.8700 (mmm) REVERT: A 362 ASP cc_start: 0.8373 (m-30) cc_final: 0.7777 (m-30) REVERT: A 375 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8544 (mmtm) REVERT: A 501 GLN cc_start: 0.9448 (tt0) cc_final: 0.9005 (tm-30) REVERT: A 586 TYR cc_start: 0.9073 (m-80) cc_final: 0.8564 (m-80) REVERT: A 588 GLN cc_start: 0.8983 (mm-40) cc_final: 0.7513 (tm-30) REVERT: A 590 SER cc_start: 0.8989 (t) cc_final: 0.8460 (p) REVERT: A 604 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8437 (tpp80) REVERT: A 630 TYR cc_start: 0.7830 (m-80) cc_final: 0.6471 (m-80) REVERT: A 645 GLN cc_start: 0.8463 (tp40) cc_final: 0.8005 (tp40) REVERT: A 650 GLN cc_start: 0.8428 (mt0) cc_final: 0.7645 (mt0) REVERT: A 664 THR cc_start: 0.9392 (p) cc_final: 0.8850 (p) REVERT: A 668 ASN cc_start: 0.8808 (m-40) cc_final: 0.8375 (m-40) REVERT: A 673 TYR cc_start: 0.9157 (t80) cc_final: 0.8673 (t80) REVERT: A 686 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7837 (tpt170) REVERT: B 23 LYS cc_start: 0.9283 (mmtm) cc_final: 0.8884 (mmmt) REVERT: B 99 LYS cc_start: 0.9352 (tptm) cc_final: 0.8992 (tptm) REVERT: B 144 MET cc_start: 0.8957 (mtm) cc_final: 0.8668 (mtm) REVERT: B 167 LEU cc_start: 0.8965 (mt) cc_final: 0.8730 (mt) REVERT: B 172 LEU cc_start: 0.8808 (mp) cc_final: 0.8504 (mp) REVERT: B 186 ILE cc_start: 0.9736 (mt) cc_final: 0.9465 (mt) REVERT: B 190 MET cc_start: 0.9365 (mtm) cc_final: 0.9126 (mtm) REVERT: B 235 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: B 274 ARG cc_start: 0.8088 (tmt-80) cc_final: 0.7442 (tpt170) REVERT: B 296 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8434 (tptt) REVERT: B 317 MET cc_start: 0.8565 (mtt) cc_final: 0.8158 (mpp) REVERT: B 319 MET cc_start: 0.8541 (tpp) cc_final: 0.8125 (tpp) REVERT: B 322 MET cc_start: 0.8181 (mmt) cc_final: 0.7854 (mmm) REVERT: B 348 MET cc_start: 0.8517 (tpp) cc_final: 0.8266 (tpt) REVERT: B 349 LEU cc_start: 0.9585 (mt) cc_final: 0.9368 (mt) REVERT: B 355 TYR cc_start: 0.8900 (m-80) cc_final: 0.8674 (m-10) REVERT: B 370 ASN cc_start: 0.9423 (m-40) cc_final: 0.9166 (m110) REVERT: B 375 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8055 (mmmm) REVERT: B 390 GLN cc_start: 0.9246 (mt0) cc_final: 0.8947 (mm-40) REVERT: B 403 ILE cc_start: 0.9285 (mm) cc_final: 0.9063 (mm) REVERT: B 430 LYS cc_start: 0.8911 (mttt) cc_final: 0.8506 (mmtt) REVERT: B 501 GLN cc_start: 0.9523 (tt0) cc_final: 0.9237 (tt0) REVERT: B 602 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 604 ARG cc_start: 0.9251 (mmp80) cc_final: 0.8972 (mmp80) REVERT: B 626 TYR cc_start: 0.7859 (m-80) cc_final: 0.7150 (m-80) REVERT: B 640 MET cc_start: 0.9015 (tpp) cc_final: 0.8679 (tpp) REVERT: B 645 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8839 (tp-100) REVERT: C 157 MET cc_start: 0.8374 (mtm) cc_final: 0.7794 (mtm) REVERT: C 162 TYR cc_start: 0.7695 (m-80) cc_final: 0.7493 (m-10) REVERT: C 177 TYR cc_start: 0.8917 (t80) cc_final: 0.8601 (t80) REVERT: D 82 ASP cc_start: 0.8804 (m-30) cc_final: 0.8388 (p0) REVERT: D 116 GLU cc_start: 0.9442 (pm20) cc_final: 0.9042 (tm-30) REVERT: D 137 MET cc_start: 0.6086 (ttt) cc_final: 0.5677 (tmm) REVERT: D 185 MET cc_start: 0.4493 (mmp) cc_final: 0.4123 (mmm) REVERT: D 230 ASP cc_start: 0.8993 (t70) cc_final: 0.8691 (p0) REVERT: D 262 TYR cc_start: 0.8628 (t80) cc_final: 0.8369 (t80) REVERT: E 25 TRP cc_start: 0.8208 (p-90) cc_final: 0.7386 (p-90) REVERT: E 34 MET cc_start: 0.9039 (mpp) cc_final: 0.8815 (ptp) outliers start: 1 outliers final: 0 residues processed: 636 average time/residue: 0.2982 time to fit residues: 283.2577 Evaluate side-chains 546 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 546 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 8.9990 chunk 191 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 overall best weight: 2.8030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 496 ASN B 668 ASN C 69 GLN C 238 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.149294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105211 restraints weight = 44888.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109024 restraints weight = 27580.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111609 restraints weight = 18860.739| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17041 Z= 0.213 Angle : 0.659 9.849 23026 Z= 0.346 Chirality : 0.044 0.184 2464 Planarity : 0.004 0.053 2931 Dihedral : 10.537 161.912 2325 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.96 (0.18), residues: 2012 helix: 1.20 (0.15), residues: 1151 sheet: -0.64 (0.36), residues: 191 loop : 0.24 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 558 HIS 0.030 0.002 HIS C 201 PHE 0.031 0.002 PHE B 129 TYR 0.034 0.002 TYR C 174 ARG 0.012 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 912) hydrogen bonds : angle 4.99632 ( 2664) SS BOND : bond 0.01271 ( 3) SS BOND : angle 4.84908 ( 6) covalent geometry : bond 0.00451 (17038) covalent geometry : angle 0.65420 (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 608 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.9369 (m-80) cc_final: 0.9158 (m-80) REVERT: A 164 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.8041 (ttm110) REVERT: A 186 ILE cc_start: 0.9565 (mm) cc_final: 0.9198 (mm) REVERT: A 190 MET cc_start: 0.9271 (mtm) cc_final: 0.8989 (mtm) REVERT: A 250 TYR cc_start: 0.7342 (m-80) cc_final: 0.6983 (m-80) REVERT: A 257 ASP cc_start: 0.8423 (m-30) cc_final: 0.8072 (m-30) REVERT: A 263 ASP cc_start: 0.9023 (m-30) cc_final: 0.8650 (m-30) REVERT: A 286 ASP cc_start: 0.9135 (m-30) cc_final: 0.8913 (m-30) REVERT: A 290 GLU cc_start: 0.9321 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 291 LEU cc_start: 0.9723 (mt) cc_final: 0.9264 (mt) REVERT: A 301 PHE cc_start: 0.8887 (m-80) cc_final: 0.8465 (m-80) REVERT: A 312 GLN cc_start: 0.8491 (tp40) cc_final: 0.8157 (tp40) REVERT: A 317 MET cc_start: 0.9056 (mmm) cc_final: 0.8587 (mmm) REVERT: A 322 MET cc_start: 0.8760 (mmm) cc_final: 0.8516 (mmm) REVERT: A 350 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7847 (mtp85) REVERT: A 362 ASP cc_start: 0.8297 (m-30) cc_final: 0.7820 (m-30) REVERT: A 375 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8542 (mmtm) REVERT: A 494 MET cc_start: 0.8353 (mmt) cc_final: 0.7988 (mmt) REVERT: A 501 GLN cc_start: 0.9502 (tt0) cc_final: 0.9043 (tm-30) REVERT: A 586 TYR cc_start: 0.9124 (m-80) cc_final: 0.8482 (m-80) REVERT: A 601 ILE cc_start: 0.9401 (tt) cc_final: 0.8962 (tt) REVERT: A 645 GLN cc_start: 0.8654 (tp40) cc_final: 0.8393 (tp40) REVERT: A 664 THR cc_start: 0.9421 (p) cc_final: 0.9016 (p) REVERT: A 668 ASN cc_start: 0.8991 (m-40) cc_final: 0.8707 (m-40) REVERT: A 686 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7637 (mmm160) REVERT: B 23 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9100 (mmtm) REVERT: B 99 LYS cc_start: 0.9469 (tptm) cc_final: 0.9208 (tptp) REVERT: B 119 GLU cc_start: 0.9307 (mp0) cc_final: 0.9015 (mp0) REVERT: B 129 PHE cc_start: 0.9406 (m-80) cc_final: 0.9055 (m-80) REVERT: B 144 MET cc_start: 0.9199 (mtm) cc_final: 0.8994 (mtm) REVERT: B 145 ILE cc_start: 0.9565 (tp) cc_final: 0.9364 (tp) REVERT: B 172 LEU cc_start: 0.8857 (mp) cc_final: 0.8600 (mp) REVERT: B 186 ILE cc_start: 0.9657 (mt) cc_final: 0.9453 (mt) REVERT: B 190 MET cc_start: 0.9414 (mtm) cc_final: 0.9148 (mtm) REVERT: B 205 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8011 (mmmm) REVERT: B 276 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8649 (mmtt) REVERT: B 317 MET cc_start: 0.8537 (mtt) cc_final: 0.8201 (mpp) REVERT: B 322 MET cc_start: 0.8224 (mmt) cc_final: 0.7952 (mmm) REVERT: B 370 ASN cc_start: 0.9487 (m-40) cc_final: 0.9193 (m110) REVERT: B 375 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 403 ILE cc_start: 0.9220 (mm) cc_final: 0.8964 (mm) REVERT: B 570 MET cc_start: 0.9234 (tpp) cc_final: 0.8632 (tpp) REVERT: B 575 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8600 (ptp-170) REVERT: B 602 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 604 ARG cc_start: 0.9325 (mmp80) cc_final: 0.8859 (mmp80) REVERT: B 640 MET cc_start: 0.9044 (tpp) cc_final: 0.8748 (tpp) REVERT: B 645 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8842 (tp-100) REVERT: B 657 PHE cc_start: 0.8839 (m-80) cc_final: 0.8478 (m-10) REVERT: C 130 TYR cc_start: 0.8959 (m-80) cc_final: 0.8583 (m-80) REVERT: C 157 MET cc_start: 0.8518 (mtm) cc_final: 0.7961 (mtm) REVERT: C 162 TYR cc_start: 0.7785 (m-80) cc_final: 0.7557 (m-10) REVERT: C 177 TYR cc_start: 0.8885 (t80) cc_final: 0.8604 (t80) REVERT: C 200 ILE cc_start: 0.8358 (pt) cc_final: 0.8122 (pt) REVERT: C 276 TYR cc_start: 0.8211 (t80) cc_final: 0.7969 (t80) REVERT: D 74 MET cc_start: 0.6895 (tpp) cc_final: 0.6494 (ptm) REVERT: D 82 ASP cc_start: 0.8862 (m-30) cc_final: 0.8447 (p0) REVERT: D 117 THR cc_start: 0.9414 (p) cc_final: 0.8914 (p) REVERT: D 137 MET cc_start: 0.6532 (ttt) cc_final: 0.6052 (tmm) REVERT: D 230 ASP cc_start: 0.8961 (t70) cc_final: 0.8645 (p0) REVERT: D 235 LEU cc_start: 0.7997 (mp) cc_final: 0.7772 (mp) REVERT: D 242 TYR cc_start: 0.9053 (t80) cc_final: 0.8644 (t80) REVERT: D 262 TYR cc_start: 0.8640 (t80) cc_final: 0.8308 (t80) REVERT: E 25 TRP cc_start: 0.8391 (p-90) cc_final: 0.7699 (p-90) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.2780 time to fit residues: 251.4718 Evaluate side-chains 526 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 467 ASN A 568 HIS ** 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 C 69 GLN 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 = 0.4058 r_free = 0.4058 target = 0.151086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106870 restraints weight = 44944.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110768 restraints weight = 27315.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113410 restraints weight = 18529.677| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5858 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= 0.135 Angle : 0.616 8.619 23026 Z= 0.321 Chirality : 0.043 0.174 2464 Planarity : 0.004 0.055 2931 Dihedral : 10.193 152.483 2325 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.19), residues: 2012 helix: 1.20 (0.15), residues: 1147 sheet: -0.44 (0.38), residues: 185 loop : 0.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 623 HIS 0.022 0.001 HIS C 201 PHE 0.028 0.002 PHE B 129 TYR 0.023 0.001 TYR A 574 ARG 0.008 0.001 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 912) hydrogen bonds : angle 4.86882 ( 2664) SS BOND : bond 0.00338 ( 3) SS BOND : angle 3.62250 ( 6) covalent geometry : bond 0.00295 (17038) covalent geometry : angle 0.61345 (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 639 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 637 time to evaluate : 1.813 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 150 GLN cc_start: 0.9130 (tp40) cc_final: 0.8921 (tp40) REVERT: A 186 ILE cc_start: 0.9543 (mm) cc_final: 0.9238 (mm) REVERT: A 188 ILE cc_start: 0.9585 (mt) cc_final: 0.9363 (mt) REVERT: A 250 TYR cc_start: 0.7293 (m-80) cc_final: 0.6897 (m-80) REVERT: A 257 ASP cc_start: 0.8533 (m-30) cc_final: 0.8067 (m-30) REVERT: A 263 ASP cc_start: 0.9111 (m-30) cc_final: 0.8744 (m-30) REVERT: A 290 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 291 LEU cc_start: 0.9687 (mt) cc_final: 0.9266 (mt) REVERT: A 301 PHE cc_start: 0.8864 (m-80) cc_final: 0.8560 (m-80) REVERT: A 312 GLN cc_start: 0.8443 (tp40) cc_final: 0.8200 (tp40) REVERT: A 320 ASN cc_start: 0.8717 (m-40) cc_final: 0.8455 (m-40) REVERT: A 322 MET cc_start: 0.8857 (mmm) cc_final: 0.8603 (mmm) REVERT: A 375 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8507 (mmtm) REVERT: A 390 GLN cc_start: 0.8470 (mm110) cc_final: 0.8148 (mm-40) REVERT: A 393 SER cc_start: 0.9130 (t) cc_final: 0.8396 (t) REVERT: A 402 GLU cc_start: 0.8220 (mp0) cc_final: 0.7593 (mp0) REVERT: A 427 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8938 (mtmm) REVERT: A 494 MET cc_start: 0.8398 (mmt) cc_final: 0.7919 (mmt) REVERT: A 501 GLN cc_start: 0.9433 (tt0) cc_final: 0.9055 (tm-30) REVERT: A 561 LEU cc_start: 0.8936 (tp) cc_final: 0.8444 (tp) REVERT: A 586 TYR cc_start: 0.9154 (m-80) cc_final: 0.8426 (m-80) REVERT: A 628 GLU cc_start: 0.9315 (tt0) cc_final: 0.8959 (tp30) REVERT: A 630 TYR cc_start: 0.7511 (m-80) cc_final: 0.5718 (m-80) REVERT: A 645 GLN cc_start: 0.8629 (tp40) cc_final: 0.8373 (tp40) REVERT: A 664 THR cc_start: 0.9419 (p) cc_final: 0.9026 (p) REVERT: A 667 LEU cc_start: 0.9334 (tt) cc_final: 0.9124 (tt) REVERT: A 668 ASN cc_start: 0.8991 (m-40) cc_final: 0.8776 (m-40) REVERT: A 686 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7646 (mmm160) REVERT: B 23 LYS cc_start: 0.9372 (mmtm) cc_final: 0.8970 (mmmt) REVERT: B 95 MET cc_start: 0.8788 (tpp) cc_final: 0.8484 (tpp) REVERT: B 99 LYS cc_start: 0.9473 (tptm) cc_final: 0.8900 (tptm) REVERT: B 124 ILE cc_start: 0.9545 (mm) cc_final: 0.9003 (mm) REVERT: B 129 PHE cc_start: 0.9428 (m-80) cc_final: 0.8970 (m-80) REVERT: B 144 MET cc_start: 0.9139 (mtm) cc_final: 0.8835 (mtm) REVERT: B 147 GLN cc_start: 0.8677 (mp10) cc_final: 0.8442 (mp10) REVERT: B 167 LEU cc_start: 0.8958 (mt) cc_final: 0.8739 (mt) REVERT: B 186 ILE cc_start: 0.9632 (mt) cc_final: 0.9414 (mt) REVERT: B 190 MET cc_start: 0.9393 (mtm) cc_final: 0.9107 (mtm) REVERT: B 205 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7900 (mmmm) REVERT: B 227 MET cc_start: 0.9273 (ptp) cc_final: 0.8547 (ptp) REVERT: B 314 MET cc_start: 0.8582 (ttt) cc_final: 0.8257 (tmm) REVERT: B 322 MET cc_start: 0.8328 (mmt) cc_final: 0.7944 (mmm) REVERT: B 348 MET cc_start: 0.8327 (tpt) cc_final: 0.7586 (tpp) REVERT: B 352 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 370 ASN cc_start: 0.9433 (m-40) cc_final: 0.9088 (m110) REVERT: B 375 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8350 (mtpt) REVERT: B 390 GLN cc_start: 0.9296 (mt0) cc_final: 0.9000 (mm-40) REVERT: B 399 GLU cc_start: 0.8996 (tp30) cc_final: 0.8450 (tp30) REVERT: B 403 ILE cc_start: 0.8947 (mm) cc_final: 0.8435 (tp) REVERT: B 475 ASN cc_start: 0.9088 (m-40) cc_final: 0.8755 (m110) REVERT: B 500 ILE cc_start: 0.9699 (tp) cc_final: 0.9438 (tp) REVERT: B 501 GLN cc_start: 0.9558 (tt0) cc_final: 0.9262 (tt0) REVERT: B 516 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8568 (tp-100) REVERT: B 550 MET cc_start: 0.8350 (mmt) cc_final: 0.8128 (mmt) REVERT: B 598 MET cc_start: 0.8559 (ttm) cc_final: 0.8256 (ttm) REVERT: B 602 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 604 ARG cc_start: 0.9326 (mmp80) cc_final: 0.9049 (mmp80) REVERT: B 624 PHE cc_start: 0.8695 (m-80) cc_final: 0.8436 (m-80) REVERT: B 634 MET cc_start: 0.9125 (mmm) cc_final: 0.8785 (mmp) REVERT: B 640 MET cc_start: 0.8974 (tpp) cc_final: 0.8729 (tpp) REVERT: B 645 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8855 (tp-100) REVERT: B 656 LEU cc_start: 0.9249 (mt) cc_final: 0.8964 (mt) REVERT: C 130 TYR cc_start: 0.8983 (m-80) cc_final: 0.8602 (m-80) REVERT: C 157 MET cc_start: 0.8310 (mtm) cc_final: 0.7931 (mtm) REVERT: C 177 TYR cc_start: 0.8800 (t80) cc_final: 0.8553 (t80) REVERT: C 200 ILE cc_start: 0.8265 (pt) cc_final: 0.7978 (pt) REVERT: C 212 ILE cc_start: 0.6238 (mt) cc_final: 0.5814 (mt) REVERT: C 276 TYR cc_start: 0.8189 (t80) cc_final: 0.7910 (t80) REVERT: D 74 MET cc_start: 0.7066 (tpp) cc_final: 0.6831 (ptm) REVERT: D 82 ASP cc_start: 0.8966 (m-30) cc_final: 0.8615 (p0) REVERT: D 137 MET cc_start: 0.6666 (ttt) cc_final: 0.6237 (tmm) REVERT: D 230 ASP cc_start: 0.8928 (t70) cc_final: 0.8601 (p0) REVERT: D 242 TYR cc_start: 0.9013 (t80) cc_final: 0.8561 (t80) REVERT: D 262 TYR cc_start: 0.8589 (t80) cc_final: 0.8337 (t80) REVERT: E 25 TRP cc_start: 0.8337 (p-90) cc_final: 0.7080 (p-90) outliers start: 2 outliers final: 0 residues processed: 637 average time/residue: 0.2793 time to fit residues: 266.6947 Evaluate side-chains 526 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** 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** C 69 GLN C 84 HIS C 132 GLN D 132 GLN D 136 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 = 0.3977 r_free = 0.3977 target = 0.143995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100643 restraints weight = 46576.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.104327 restraints weight = 28781.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106854 restraints weight = 19731.701| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17041 Z= 0.268 Angle : 0.718 8.810 23026 Z= 0.376 Chirality : 0.046 0.183 2464 Planarity : 0.004 0.052 2931 Dihedral : 10.312 158.280 2325 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.63 (0.18), residues: 2012 helix: 0.92 (0.15), residues: 1152 sheet: -0.63 (0.38), residues: 183 loop : 0.08 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 623 HIS 0.017 0.002 HIS C 201 PHE 0.024 0.002 PHE A 234 TYR 0.028 0.002 TYR A 574 ARG 0.014 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 912) hydrogen bonds : angle 5.17016 ( 2664) SS BOND : bond 0.00311 ( 3) SS BOND : angle 4.12845 ( 6) covalent geometry : bond 0.00570 (17038) covalent geometry : angle 0.71527 (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 594 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.9465 (t80) cc_final: 0.9265 (t80) REVERT: A 143 LEU cc_start: 0.9640 (tp) cc_final: 0.9415 (tp) REVERT: A 147 GLN cc_start: 0.9228 (tt0) cc_final: 0.8767 (tp40) REVERT: A 161 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7594 (ptm160) REVERT: A 186 ILE cc_start: 0.9558 (mm) cc_final: 0.9323 (mm) REVERT: A 190 MET cc_start: 0.9293 (mtm) cc_final: 0.8977 (mtm) REVERT: A 236 TYR cc_start: 0.9056 (t80) cc_final: 0.8669 (t80) REVERT: A 250 TYR cc_start: 0.7148 (m-80) cc_final: 0.6818 (m-80) REVERT: A 257 ASP cc_start: 0.8437 (m-30) cc_final: 0.8052 (m-30) REVERT: A 263 ASP cc_start: 0.9007 (m-30) cc_final: 0.8645 (m-30) REVERT: A 301 PHE cc_start: 0.8870 (m-80) cc_final: 0.8561 (m-80) REVERT: A 312 GLN cc_start: 0.8486 (tp40) cc_final: 0.8251 (tp40) REVERT: A 316 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 322 MET cc_start: 0.8820 (mmm) cc_final: 0.8579 (mmm) REVERT: A 362 ASP cc_start: 0.8516 (m-30) cc_final: 0.8103 (m-30) REVERT: A 366 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8944 (ptpp) REVERT: A 393 SER cc_start: 0.9191 (t) cc_final: 0.8258 (t) REVERT: A 402 GLU cc_start: 0.8332 (mp0) cc_final: 0.7630 (mp0) REVERT: A 501 GLN cc_start: 0.9473 (tt0) cc_final: 0.9142 (tm-30) REVERT: A 586 TYR cc_start: 0.9210 (m-80) cc_final: 0.8675 (m-80) REVERT: A 599 GLU cc_start: 0.9098 (pt0) cc_final: 0.8617 (pt0) REVERT: A 601 ILE cc_start: 0.9431 (tt) cc_final: 0.9084 (tt) REVERT: A 628 GLU cc_start: 0.9414 (tt0) cc_final: 0.8994 (tp30) REVERT: A 664 THR cc_start: 0.9448 (p) cc_final: 0.9089 (p) REVERT: A 668 ASN cc_start: 0.9212 (m-40) cc_final: 0.8867 (m-40) REVERT: A 683 TYR cc_start: 0.8025 (t80) cc_final: 0.7800 (t80) REVERT: A 686 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7299 (mmm160) REVERT: B 99 LYS cc_start: 0.9522 (tptm) cc_final: 0.9227 (tptp) REVERT: B 119 GLU cc_start: 0.9311 (mp0) cc_final: 0.9049 (mp0) REVERT: B 129 PHE cc_start: 0.9420 (m-80) cc_final: 0.8989 (m-80) REVERT: B 167 LEU cc_start: 0.9033 (mt) cc_final: 0.8764 (mt) REVERT: B 205 LYS cc_start: 0.8316 (mmmt) cc_final: 0.8043 (mmtm) REVERT: B 227 MET cc_start: 0.9192 (ptp) cc_final: 0.8621 (ptp) REVERT: B 322 MET cc_start: 0.8255 (mmt) cc_final: 0.7960 (mmm) REVERT: B 370 ASN cc_start: 0.9513 (m-40) cc_final: 0.9178 (m110) REVERT: B 375 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8406 (mtpt) REVERT: B 377 LYS cc_start: 0.7668 (mttt) cc_final: 0.7302 (mttp) REVERT: B 403 ILE cc_start: 0.9105 (mm) cc_final: 0.8866 (mm) REVERT: B 426 GLU cc_start: 0.9113 (tp30) cc_final: 0.8737 (tp30) REVERT: B 475 ASN cc_start: 0.9373 (m-40) cc_final: 0.9084 (m110) REVERT: B 501 GLN cc_start: 0.9539 (tt0) cc_final: 0.9219 (tt0) REVERT: B 586 TYR cc_start: 0.9558 (m-80) cc_final: 0.9264 (m-80) REVERT: B 598 MET cc_start: 0.8624 (ttm) cc_final: 0.8325 (ttm) REVERT: B 602 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 640 MET cc_start: 0.8992 (tpp) cc_final: 0.8737 (tpp) REVERT: B 645 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8719 (tp-100) REVERT: C 157 MET cc_start: 0.8414 (mtm) cc_final: 0.8029 (mtm) REVERT: C 162 TYR cc_start: 0.7412 (m-10) cc_final: 0.7166 (m-10) REVERT: C 177 TYR cc_start: 0.8748 (t80) cc_final: 0.8473 (t80) REVERT: C 197 ASP cc_start: 0.7882 (m-30) cc_final: 0.6903 (m-30) REVERT: C 200 ILE cc_start: 0.8189 (pt) cc_final: 0.7779 (pt) REVERT: C 201 HIS cc_start: 0.7471 (m-70) cc_final: 0.7126 (t-170) REVERT: C 237 GLU cc_start: 0.9620 (mp0) cc_final: 0.9393 (pp20) REVERT: C 276 TYR cc_start: 0.8406 (t80) cc_final: 0.8137 (t80) REVERT: D 74 MET cc_start: 0.7381 (tpp) cc_final: 0.6469 (ptt) REVERT: D 82 ASP cc_start: 0.8992 (m-30) cc_final: 0.8642 (p0) REVERT: D 137 MET cc_start: 0.6853 (ttt) cc_final: 0.6432 (tmm) REVERT: D 230 ASP cc_start: 0.8904 (t70) cc_final: 0.8285 (m-30) REVERT: D 235 LEU cc_start: 0.7964 (mp) cc_final: 0.7346 (mt) REVERT: D 242 TYR cc_start: 0.9048 (t80) cc_final: 0.8644 (t80) REVERT: D 262 TYR cc_start: 0.8808 (t80) cc_final: 0.8558 (t80) REVERT: E 25 TRP cc_start: 0.8397 (p-90) cc_final: 0.7688 (p-90) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.2720 time to fit residues: 243.1977 Evaluate side-chains 495 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 0.0370 chunk 149 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 474 GLN ** 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** C 69 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103936 restraints weight = 45913.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107727 restraints weight = 28409.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110336 restraints weight = 19170.158| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17041 Z= 0.165 Angle : 0.666 8.702 23026 Z= 0.347 Chirality : 0.044 0.177 2464 Planarity : 0.004 0.063 2931 Dihedral : 10.043 153.772 2325 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.18), residues: 2012 helix: 1.01 (0.15), residues: 1132 sheet: -0.66 (0.37), residues: 193 loop : -0.01 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 30 HIS 0.018 0.001 HIS C 201 PHE 0.022 0.002 PHE A 492 TYR 0.023 0.002 TYR A 574 ARG 0.010 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 912) hydrogen bonds : angle 5.08965 ( 2664) SS BOND : bond 0.00551 ( 3) SS BOND : angle 4.48532 ( 6) covalent geometry : bond 0.00371 (17038) covalent geometry : angle 0.66226 (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 610 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9194 (tt0) cc_final: 0.8781 (tp40) REVERT: A 157 LEU cc_start: 0.9182 (tp) cc_final: 0.8939 (tp) REVERT: A 164 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8481 (ttp80) REVERT: A 186 ILE cc_start: 0.9514 (mm) cc_final: 0.9255 (mm) REVERT: A 190 MET cc_start: 0.9311 (mtm) cc_final: 0.9013 (mtm) REVERT: A 250 TYR cc_start: 0.7124 (m-80) cc_final: 0.6670 (m-80) REVERT: A 257 ASP cc_start: 0.8336 (m-30) cc_final: 0.7854 (m-30) REVERT: A 263 ASP cc_start: 0.9079 (m-30) cc_final: 0.8733 (m-30) REVERT: A 290 GLU cc_start: 0.8818 (pp20) cc_final: 0.8154 (pp20) REVERT: A 291 LEU cc_start: 0.9584 (mt) cc_final: 0.9257 (mt) REVERT: A 301 PHE cc_start: 0.8820 (m-80) cc_final: 0.8591 (m-80) REVERT: A 312 GLN cc_start: 0.8458 (tp40) cc_final: 0.8172 (tp40) REVERT: A 316 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 375 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8211 (mmtm) REVERT: A 447 ASN cc_start: 0.8951 (m-40) cc_final: 0.8720 (m-40) REVERT: A 479 TYR cc_start: 0.8507 (t80) cc_final: 0.7962 (t80) REVERT: A 501 GLN cc_start: 0.9467 (tt0) cc_final: 0.9099 (tm-30) REVERT: A 586 TYR cc_start: 0.9194 (m-80) cc_final: 0.8726 (m-80) REVERT: A 628 GLU cc_start: 0.9389 (tt0) cc_final: 0.9006 (mm-30) REVERT: A 664 THR cc_start: 0.9457 (p) cc_final: 0.9107 (p) REVERT: A 668 ASN cc_start: 0.9062 (m-40) cc_final: 0.8845 (m-40) REVERT: A 686 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7351 (mmm160) REVERT: B 40 TYR cc_start: 0.9247 (t80) cc_final: 0.9032 (t80) REVERT: B 99 LYS cc_start: 0.9446 (tptm) cc_final: 0.9237 (tptp) REVERT: B 119 GLU cc_start: 0.9281 (mp0) cc_final: 0.9047 (mp0) REVERT: B 129 PHE cc_start: 0.9379 (m-80) cc_final: 0.8998 (m-80) REVERT: B 167 LEU cc_start: 0.9013 (mt) cc_final: 0.8695 (mt) REVERT: B 174 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7737 (tp30) REVERT: B 227 MET cc_start: 0.9190 (ptp) cc_final: 0.8590 (ptp) REVERT: B 235 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: B 274 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8248 (mmm160) REVERT: B 322 MET cc_start: 0.8361 (mmt) cc_final: 0.8004 (mmm) REVERT: B 348 MET cc_start: 0.8387 (tpt) cc_final: 0.8094 (tpp) REVERT: B 370 ASN cc_start: 0.9472 (m-40) cc_final: 0.9037 (m110) REVERT: B 375 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8436 (mtpt) REVERT: B 377 LYS cc_start: 0.7794 (mttt) cc_final: 0.7498 (mttp) REVERT: B 387 GLN cc_start: 0.9080 (mt0) cc_final: 0.8361 (mp10) REVERT: B 426 GLU cc_start: 0.9115 (tp30) cc_final: 0.8671 (tp30) REVERT: B 445 ILE cc_start: 0.8973 (mm) cc_final: 0.8564 (mm) REVERT: B 456 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8559 (mmtm) REVERT: B 475 ASN cc_start: 0.9142 (m-40) cc_final: 0.8758 (m110) REVERT: B 501 GLN cc_start: 0.9540 (tt0) cc_final: 0.9203 (tt0) REVERT: B 516 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8313 (tp-100) REVERT: B 570 MET cc_start: 0.9398 (mmm) cc_final: 0.8643 (tpp) REVERT: B 598 MET cc_start: 0.8585 (ttm) cc_final: 0.8291 (ttm) REVERT: B 602 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 604 ARG cc_start: 0.9334 (mmp80) cc_final: 0.8695 (mmp80) REVERT: B 645 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8763 (tp-100) REVERT: B 677 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.7790 (mmm160) REVERT: C 157 MET cc_start: 0.8355 (mtm) cc_final: 0.7996 (mtm) REVERT: C 162 TYR cc_start: 0.7357 (m-10) cc_final: 0.7134 (m-10) REVERT: C 177 TYR cc_start: 0.8811 (t80) cc_final: 0.8577 (t80) REVERT: C 200 ILE cc_start: 0.8283 (pt) cc_final: 0.7964 (pt) REVERT: C 212 ILE cc_start: 0.6626 (mt) cc_final: 0.6326 (mt) REVERT: C 276 TYR cc_start: 0.8412 (t80) cc_final: 0.8174 (t80) REVERT: D 74 MET cc_start: 0.7700 (tpp) cc_final: 0.6890 (ptt) REVERT: D 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.8693 (p0) REVERT: D 116 GLU cc_start: 0.9449 (pm20) cc_final: 0.9046 (tm-30) REVERT: D 137 MET cc_start: 0.6750 (ttt) cc_final: 0.6464 (ppp) REVERT: D 230 ASP cc_start: 0.8935 (t70) cc_final: 0.8383 (m-30) REVERT: D 242 TYR cc_start: 0.9111 (t80) cc_final: 0.8690 (t80) REVERT: E 25 TRP cc_start: 0.8352 (p-90) cc_final: 0.7638 (p-90) REVERT: E 63 THR cc_start: 0.9304 (t) cc_final: 0.9024 (t) REVERT: E 97 GLN cc_start: 0.8940 (mt0) cc_final: 0.8726 (mp10) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.2734 time to fit residues: 250.9275 Evaluate side-chains 512 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 216 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100207 restraints weight = 47098.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103890 restraints weight = 28967.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106380 restraints weight = 19883.100| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17041 Z= 0.287 Angle : 0.751 10.286 23026 Z= 0.396 Chirality : 0.047 0.235 2464 Planarity : 0.004 0.059 2931 Dihedral : 10.263 159.815 2325 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.30 (0.18), residues: 2012 helix: 0.64 (0.15), residues: 1157 sheet: -0.72 (0.38), residues: 177 loop : -0.07 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 30 HIS 0.016 0.002 HIS C 201 PHE 0.026 0.002 PHE A 378 TYR 0.025 0.002 TYR D 105 ARG 0.007 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 912) hydrogen bonds : angle 5.43312 ( 2664) SS BOND : bond 0.00895 ( 3) SS BOND : angle 5.03725 ( 6) covalent geometry : bond 0.00612 (17038) covalent geometry : angle 0.74634 (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 578 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 2.021 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 128 PHE cc_start: 0.9460 (t80) cc_final: 0.9213 (t80) REVERT: A 143 LEU cc_start: 0.9666 (tp) cc_final: 0.9427 (tp) REVERT: A 157 LEU cc_start: 0.9315 (tp) cc_final: 0.9083 (tp) REVERT: A 186 ILE cc_start: 0.9526 (mm) cc_final: 0.9253 (mm) REVERT: A 190 MET cc_start: 0.9294 (mtm) cc_final: 0.9014 (mtm) REVERT: A 236 TYR cc_start: 0.9109 (t80) cc_final: 0.8731 (t80) REVERT: A 250 TYR cc_start: 0.7195 (m-80) cc_final: 0.6818 (m-80) REVERT: A 257 ASP cc_start: 0.8405 (m-30) cc_final: 0.8062 (m-30) REVERT: A 263 ASP cc_start: 0.9060 (m-30) cc_final: 0.8724 (m-30) REVERT: A 290 GLU cc_start: 0.8849 (pp20) cc_final: 0.8163 (pp20) REVERT: A 291 LEU cc_start: 0.9601 (mt) cc_final: 0.9208 (mt) REVERT: A 301 PHE cc_start: 0.8918 (m-80) cc_final: 0.8636 (m-80) REVERT: A 312 GLN cc_start: 0.8472 (tp40) cc_final: 0.8111 (tp-100) REVERT: A 316 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 362 ASP cc_start: 0.8284 (m-30) cc_final: 0.7863 (m-30) REVERT: A 447 ASN cc_start: 0.8828 (m-40) cc_final: 0.8554 (m-40) REVERT: A 474 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8695 (mm110) REVERT: A 479 TYR cc_start: 0.8397 (t80) cc_final: 0.8192 (t80) REVERT: A 501 GLN cc_start: 0.9473 (tt0) cc_final: 0.9109 (tm-30) REVERT: A 586 TYR cc_start: 0.9187 (m-80) cc_final: 0.8720 (m-80) REVERT: A 628 GLU cc_start: 0.9396 (tt0) cc_final: 0.9037 (tp30) REVERT: A 632 MET cc_start: 0.8436 (mtp) cc_final: 0.7728 (mtm) REVERT: A 662 MET cc_start: 0.9118 (pmm) cc_final: 0.8696 (pmm) REVERT: A 664 THR cc_start: 0.9443 (p) cc_final: 0.9082 (p) REVERT: A 668 ASN cc_start: 0.9270 (m-40) cc_final: 0.8867 (m-40) REVERT: B 40 TYR cc_start: 0.9285 (t80) cc_final: 0.9035 (t80) REVERT: B 99 LYS cc_start: 0.9483 (tptm) cc_final: 0.9252 (tptm) REVERT: B 119 GLU cc_start: 0.9388 (mp0) cc_final: 0.9140 (mp0) REVERT: B 150 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8717 (tp-100) REVERT: B 167 LEU cc_start: 0.9066 (mt) cc_final: 0.8807 (mt) REVERT: B 174 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7608 (tp30) REVERT: B 184 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8747 (ttp-170) REVERT: B 218 ASN cc_start: 0.9422 (t0) cc_final: 0.9204 (t0) REVERT: B 227 MET cc_start: 0.9127 (ptp) cc_final: 0.8592 (ptp) REVERT: B 236 TYR cc_start: 0.8652 (t80) cc_final: 0.8414 (t80) REVERT: B 274 ARG cc_start: 0.8544 (mmm160) cc_final: 0.8239 (mmm160) REVERT: B 276 LYS cc_start: 0.8446 (mmtm) cc_final: 0.7892 (mmtm) REVERT: B 349 LEU cc_start: 0.9587 (mt) cc_final: 0.9361 (mt) REVERT: B 370 ASN cc_start: 0.9511 (m-40) cc_final: 0.9080 (m110) REVERT: B 375 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8588 (mtpt) REVERT: B 377 LYS cc_start: 0.7660 (mttt) cc_final: 0.7446 (mttp) REVERT: B 426 GLU cc_start: 0.9066 (tp30) cc_final: 0.8525 (tp30) REVERT: B 437 THR cc_start: 0.9605 (m) cc_final: 0.9402 (m) REVERT: B 475 ASN cc_start: 0.9426 (m-40) cc_final: 0.9224 (m110) REVERT: B 501 GLN cc_start: 0.9565 (tt0) cc_final: 0.9211 (tt0) REVERT: B 570 MET cc_start: 0.9432 (mmm) cc_final: 0.8759 (mmt) REVERT: B 586 TYR cc_start: 0.9537 (m-80) cc_final: 0.9201 (m-80) REVERT: B 598 MET cc_start: 0.8654 (ttm) cc_final: 0.8408 (ttm) REVERT: B 645 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8767 (tp-100) REVERT: C 21 PHE cc_start: 0.9354 (m-80) cc_final: 0.9120 (m-80) REVERT: C 157 MET cc_start: 0.8397 (mtm) cc_final: 0.7955 (mtm) REVERT: C 197 ASP cc_start: 0.7902 (m-30) cc_final: 0.7075 (m-30) REVERT: C 200 ILE cc_start: 0.8251 (pt) cc_final: 0.7872 (pt) REVERT: C 201 HIS cc_start: 0.7619 (m-70) cc_final: 0.7240 (t-170) REVERT: C 276 TYR cc_start: 0.8443 (t80) cc_final: 0.8232 (t80) REVERT: D 117 THR cc_start: 0.9466 (p) cc_final: 0.9007 (p) REVERT: D 137 MET cc_start: 0.6896 (ttt) cc_final: 0.6572 (tmm) REVERT: D 230 ASP cc_start: 0.8915 (t70) cc_final: 0.8318 (m-30) REVERT: D 242 TYR cc_start: 0.9103 (t80) cc_final: 0.8587 (t80) REVERT: D 262 TYR cc_start: 0.8984 (t80) cc_final: 0.8752 (t80) REVERT: E 25 TRP cc_start: 0.8422 (p-90) cc_final: 0.7184 (p-90) REVERT: E 67 TYR cc_start: 0.8976 (m-80) cc_final: 0.8432 (m-80) REVERT: E 97 GLN cc_start: 0.8967 (mt0) cc_final: 0.8748 (mp10) outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 0.2811 time to fit residues: 243.0636 Evaluate side-chains 487 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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: 7.9990 chunk 85 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 467 ASN A 474 GLN ** A 588 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3993 r_free = 0.3993 target = 0.145216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101589 restraints weight = 46596.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105353 restraints weight = 28796.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107956 restraints weight = 19722.083| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.7188 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= 0.188 Angle : 0.713 11.726 23026 Z= 0.371 Chirality : 0.046 0.199 2464 Planarity : 0.004 0.053 2931 Dihedral : 10.107 155.113 2325 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.06 % Allowed : 0.61 % Favored : 99.33 % 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: 0.31 (0.18), residues: 2012 helix: 0.67 (0.15), residues: 1152 sheet: -0.69 (0.39), residues: 177 loop : -0.12 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 44 HIS 0.015 0.002 HIS C 201 PHE 0.024 0.002 PHE A 492 TYR 0.023 0.002 TYR A 574 ARG 0.014 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 912) hydrogen bonds : angle 5.35207 ( 2664) SS BOND : bond 0.00736 ( 3) SS BOND : angle 5.16597 ( 6) covalent geometry : bond 0.00416 (17038) covalent geometry : angle 0.70789 (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 598 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 597 time to evaluate : 1.925 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: 0.8411 (ttp80) cc_final: 0.8167 (ttp80) REVERT: A 186 ILE cc_start: 0.9527 (mm) cc_final: 0.9280 (mm) REVERT: A 190 MET cc_start: 0.9283 (mtm) cc_final: 0.9019 (mtm) REVERT: A 250 TYR cc_start: 0.7159 (m-80) cc_final: 0.6768 (m-80) REVERT: A 257 ASP cc_start: 0.8504 (m-30) cc_final: 0.7945 (m-30) REVERT: A 263 ASP cc_start: 0.9056 (m-30) cc_final: 0.8741 (m-30) REVERT: A 290 GLU cc_start: 0.8796 (pp20) cc_final: 0.8071 (pp20) REVERT: A 291 LEU cc_start: 0.9589 (mt) cc_final: 0.9259 (mt) REVERT: A 301 PHE cc_start: 0.8852 (m-80) cc_final: 0.8552 (m-80) REVERT: A 312 GLN cc_start: 0.8417 (tp40) cc_final: 0.8052 (tp-100) REVERT: A 316 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 375 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8548 (mmtm) REVERT: A 447 ASN cc_start: 0.8788 (m-40) cc_final: 0.8544 (m-40) REVERT: A 501 GLN cc_start: 0.9465 (tt0) cc_final: 0.9105 (tm-30) REVERT: A 586 TYR cc_start: 0.9181 (m-80) cc_final: 0.8844 (m-80) REVERT: A 615 MET cc_start: 0.8912 (mmp) cc_final: 0.8583 (mmp) REVERT: A 628 GLU cc_start: 0.9353 (tt0) cc_final: 0.9072 (tp30) REVERT: A 632 MET cc_start: 0.8379 (mtp) cc_final: 0.7938 (mtp) REVERT: A 662 MET cc_start: 0.9101 (pmm) cc_final: 0.8640 (pmm) REVERT: A 664 THR cc_start: 0.9416 (p) cc_final: 0.9027 (p) REVERT: A 686 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7558 (mmm160) REVERT: B 18 ILE cc_start: 0.9234 (mm) cc_final: 0.8915 (mm) REVERT: B 25 GLN cc_start: 0.8570 (mt0) cc_final: 0.8311 (mt0) REVERT: B 40 TYR cc_start: 0.9276 (t80) cc_final: 0.9048 (t80) REVERT: B 99 LYS cc_start: 0.9444 (tptm) cc_final: 0.9181 (tptp) REVERT: B 119 GLU cc_start: 0.9341 (mp0) cc_final: 0.9096 (mp0) REVERT: B 129 PHE cc_start: 0.9422 (m-80) cc_final: 0.9125 (m-80) REVERT: B 167 LEU cc_start: 0.8985 (mt) cc_final: 0.8720 (mt) REVERT: B 174 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7727 (tp30) REVERT: B 227 MET cc_start: 0.9129 (ptp) cc_final: 0.8602 (ptp) REVERT: B 263 ASP cc_start: 0.9489 (m-30) cc_final: 0.9183 (m-30) REVERT: B 274 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8276 (mmm160) REVERT: B 276 LYS cc_start: 0.8402 (mmtm) cc_final: 0.7885 (mptt) REVERT: B 312 GLN cc_start: 0.8495 (pm20) cc_final: 0.8222 (pm20) REVERT: B 322 MET cc_start: 0.8642 (mmm) cc_final: 0.8394 (mmm) REVERT: B 344 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 348 MET cc_start: 0.8438 (tpt) cc_final: 0.8199 (tpp) REVERT: B 370 ASN cc_start: 0.9483 (m-40) cc_final: 0.9027 (m110) REVERT: B 375 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8543 (mtpt) REVERT: B 377 LYS cc_start: 0.7733 (mttt) cc_final: 0.7498 (mttp) REVERT: B 387 GLN cc_start: 0.9127 (mt0) cc_final: 0.8560 (mp10) REVERT: B 390 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8908 (mm-40) REVERT: B 426 GLU cc_start: 0.9086 (tp30) cc_final: 0.8408 (tp30) REVERT: B 475 ASN cc_start: 0.9216 (m-40) cc_final: 0.8773 (m110) REVERT: B 483 GLU cc_start: 0.9364 (pm20) cc_final: 0.9156 (pm20) REVERT: B 501 GLN cc_start: 0.9548 (tt0) cc_final: 0.9211 (tt0) REVERT: B 516 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8461 (tp-100) REVERT: B 570 MET cc_start: 0.9475 (mmm) cc_final: 0.8754 (tpp) REVERT: B 586 TYR cc_start: 0.9521 (m-80) cc_final: 0.9173 (m-80) REVERT: B 598 MET cc_start: 0.8504 (ttm) cc_final: 0.8232 (ttm) REVERT: B 602 GLU cc_start: 0.8656 (tp30) cc_final: 0.8223 (mm-30) REVERT: B 624 PHE cc_start: 0.8902 (m-80) cc_final: 0.8597 (m-80) REVERT: B 645 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8834 (tp-100) REVERT: C 157 MET cc_start: 0.8182 (mtm) cc_final: 0.7944 (mtm) REVERT: C 197 ASP cc_start: 0.7721 (m-30) cc_final: 0.6347 (m-30) REVERT: C 200 ILE cc_start: 0.8283 (pt) cc_final: 0.7890 (pt) REVERT: D 137 MET cc_start: 0.6931 (ttt) cc_final: 0.6710 (tmm) REVERT: D 230 ASP cc_start: 0.8893 (t70) cc_final: 0.8287 (m-30) REVERT: D 242 TYR cc_start: 0.9068 (t80) cc_final: 0.8574 (t80) REVERT: D 262 TYR cc_start: 0.9002 (t80) cc_final: 0.8756 (t80) REVERT: E 25 TRP cc_start: 0.8351 (p-90) cc_final: 0.7163 (p-90) REVERT: E 97 GLN cc_start: 0.8971 (mt0) cc_final: 0.8747 (mp10) outliers start: 1 outliers final: 1 residues processed: 597 average time/residue: 0.2774 time to fit residues: 249.4017 Evaluate side-chains 505 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 390 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** 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 475 ASN C 69 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104359 restraints weight = 46263.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108306 restraints weight = 28515.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111001 restraints weight = 19278.654| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17041 Z= 0.157 Angle : 0.711 12.072 23026 Z= 0.371 Chirality : 0.046 0.200 2464 Planarity : 0.004 0.053 2931 Dihedral : 9.871 149.722 2325 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: 0.32 (0.18), residues: 2012 helix: 0.74 (0.15), residues: 1151 sheet: -0.83 (0.38), residues: 175 loop : -0.20 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 30 HIS 0.005 0.001 HIS B 469 PHE 0.028 0.002 PHE A 100 TYR 0.021 0.002 TYR B 310 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 912) hydrogen bonds : angle 5.28410 ( 2664) SS BOND : bond 0.00685 ( 3) SS BOND : angle 5.22816 ( 6) covalent geometry : bond 0.00348 (17038) covalent geometry : angle 0.70560 (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 588 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8615 (m-80) cc_final: 0.8172 (m-80) REVERT: A 147 GLN cc_start: 0.9102 (tt0) cc_final: 0.8545 (tp40) REVERT: A 164 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8123 (ttp80) REVERT: A 186 ILE cc_start: 0.9535 (mm) cc_final: 0.9309 (mm) REVERT: A 188 ILE cc_start: 0.9570 (mt) cc_final: 0.9270 (mt) REVERT: A 190 MET cc_start: 0.9291 (mtm) cc_final: 0.9006 (mtm) REVERT: A 250 TYR cc_start: 0.7257 (m-80) cc_final: 0.6872 (m-80) REVERT: A 257 ASP cc_start: 0.8464 (m-30) cc_final: 0.8127 (m-30) REVERT: A 263 ASP cc_start: 0.9097 (m-30) cc_final: 0.8730 (m-30) REVERT: A 290 GLU cc_start: 0.8732 (pp20) cc_final: 0.7999 (pp20) REVERT: A 291 LEU cc_start: 0.9556 (mt) cc_final: 0.9203 (mt) REVERT: A 301 PHE cc_start: 0.8738 (m-80) cc_final: 0.8407 (m-80) REVERT: A 316 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 322 MET cc_start: 0.8891 (mmm) cc_final: 0.8656 (mmm) REVERT: A 375 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8417 (mmtm) REVERT: A 447 ASN cc_start: 0.8773 (m-40) cc_final: 0.8533 (m-40) REVERT: A 467 ASN cc_start: 0.8939 (t0) cc_final: 0.8730 (t0) REVERT: A 501 GLN cc_start: 0.9455 (tt0) cc_final: 0.9096 (tm-30) REVERT: A 586 TYR cc_start: 0.9125 (m-80) cc_final: 0.8859 (m-80) REVERT: A 601 ILE cc_start: 0.9427 (tt) cc_final: 0.9133 (tt) REVERT: A 615 MET cc_start: 0.8922 (mmp) cc_final: 0.8414 (mmp) REVERT: A 632 MET cc_start: 0.8494 (mtp) cc_final: 0.7980 (mtp) REVERT: A 655 THR cc_start: 0.9065 (m) cc_final: 0.8833 (m) REVERT: A 683 TYR cc_start: 0.8107 (t80) cc_final: 0.7772 (t80) REVERT: A 686 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7278 (mmm160) REVERT: B 40 TYR cc_start: 0.9263 (t80) cc_final: 0.9034 (t80) REVERT: B 99 LYS cc_start: 0.9469 (tptm) cc_final: 0.8868 (tptp) REVERT: B 119 GLU cc_start: 0.9289 (mp0) cc_final: 0.9063 (mp0) REVERT: B 129 PHE cc_start: 0.9391 (m-80) cc_final: 0.9060 (m-80) REVERT: B 167 LEU cc_start: 0.9007 (mt) cc_final: 0.8715 (mt) REVERT: B 174 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7819 (tp30) REVERT: B 227 MET cc_start: 0.9157 (ptp) cc_final: 0.8611 (ptp) REVERT: B 274 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8360 (mmm160) REVERT: B 276 LYS cc_start: 0.8413 (mmtm) cc_final: 0.7955 (mmtm) REVERT: B 344 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 348 MET cc_start: 0.8430 (tpt) cc_final: 0.8205 (tpp) REVERT: B 350 ARG cc_start: 0.8923 (mmm160) cc_final: 0.8579 (mmm160) REVERT: B 370 ASN cc_start: 0.9453 (m-40) cc_final: 0.9006 (m110) REVERT: B 375 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8576 (mtpt) REVERT: B 387 GLN cc_start: 0.9078 (mt0) cc_final: 0.8601 (mp10) REVERT: B 426 GLU cc_start: 0.9092 (tp30) cc_final: 0.8515 (tp30) REVERT: B 427 LYS cc_start: 0.9378 (mppt) cc_final: 0.9165 (mmtm) REVERT: B 479 TYR cc_start: 0.8474 (t80) cc_final: 0.8217 (t80) REVERT: B 483 GLU cc_start: 0.9389 (pm20) cc_final: 0.9181 (pm20) REVERT: B 493 MET cc_start: 0.9266 (tmm) cc_final: 0.9045 (tmm) REVERT: B 501 GLN cc_start: 0.9520 (tt0) cc_final: 0.9190 (tt0) REVERT: B 550 MET cc_start: 0.7609 (mmt) cc_final: 0.7318 (mmt) REVERT: B 570 MET cc_start: 0.9471 (mmm) cc_final: 0.8617 (tpp) REVERT: B 598 MET cc_start: 0.8382 (ttm) cc_final: 0.8121 (ttm) REVERT: B 602 GLU cc_start: 0.8728 (tp30) cc_final: 0.7725 (mm-30) REVERT: B 604 ARG cc_start: 0.9378 (mmp80) cc_final: 0.9124 (mmp80) REVERT: B 624 PHE cc_start: 0.8992 (m-80) cc_final: 0.8680 (m-80) REVERT: B 634 MET cc_start: 0.9216 (mmm) cc_final: 0.8337 (mmm) REVERT: B 637 VAL cc_start: 0.9458 (t) cc_final: 0.9244 (t) REVERT: B 645 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8855 (tp-100) REVERT: B 677 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8384 (mmm-85) REVERT: C 157 MET cc_start: 0.8111 (mtm) cc_final: 0.7812 (mtm) REVERT: C 162 TYR cc_start: 0.7374 (m-10) cc_final: 0.7067 (m-10) REVERT: C 200 ILE cc_start: 0.8284 (pt) cc_final: 0.8017 (pt) REVERT: C 212 ILE cc_start: 0.5506 (mm) cc_final: 0.5116 (mm) REVERT: C 227 PHE cc_start: 0.8464 (m-80) cc_final: 0.8196 (m-80) REVERT: C 276 TYR cc_start: 0.8672 (t80) cc_final: 0.8350 (t80) REVERT: D 137 MET cc_start: 0.7041 (ttt) cc_final: 0.6794 (tmm) REVERT: D 230 ASP cc_start: 0.8830 (t70) cc_final: 0.8443 (p0) REVERT: D 242 TYR cc_start: 0.9094 (t80) cc_final: 0.8739 (t80) REVERT: D 262 TYR cc_start: 0.8996 (t80) cc_final: 0.8747 (t80) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.2713 time to fit residues: 241.8864 Evaluate side-chains 506 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 198 optimal weight: 0.0470 chunk 146 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 390 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 69 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4015 r_free = 0.4015 target = 0.147234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102729 restraints weight = 46582.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106698 restraints weight = 28573.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109482 restraints weight = 19282.193| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17041 Z= 0.176 Angle : 0.724 11.792 23026 Z= 0.375 Chirality : 0.046 0.225 2464 Planarity : 0.004 0.053 2931 Dihedral : 9.832 151.455 2325 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.18), residues: 2012 helix: 0.66 (0.15), residues: 1150 sheet: -0.69 (0.39), residues: 173 loop : -0.19 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 30 HIS 0.007 0.001 HIS C 201 PHE 0.023 0.002 PHE D 92 TYR 0.020 0.002 TYR C 242 ARG 0.005 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 912) hydrogen bonds : angle 5.32034 ( 2664) SS BOND : bond 0.00819 ( 3) SS BOND : angle 5.10547 ( 6) covalent geometry : bond 0.00394 (17038) covalent geometry : angle 0.71893 (23020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6988.17 seconds wall clock time: 122 minutes 48.11 seconds (7368.11 seconds total)