Starting phenix.real_space_refine on Sun May 18 04:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxs_45010/05_2025/9bxs_45010.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10641 2.51 5 N 2712 2.21 5 O 3216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-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: 9.17, per 1000 atoms: 0.55 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 136.89, 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: 3.92 Conformation dependent library (CDL) restraints added in 1.9 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: 1.61 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: 3.770A 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: 4.066A 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: 3.662A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A 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: 3.567A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.059A 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: 4.045A 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: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.601A 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: 4.256A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.567A 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: 4.874A 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: 3.527A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A 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: 7.540A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.473A 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: 6.485A 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: 6.479A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.587A 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: 6.147A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A 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: 5.385A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4866 1.33 - 1.46: 3195 1.46 - 1.58: 8788 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 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+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 8.74e+00 bond pdb=" CZ ARG B 600 " pdb=" NH2 ARG B 600 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.31e+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 7.12e+00 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22235 2.09 - 4.19: 715 4.19 - 6.28: 63 6.28 - 8.38: 5 8.38 - 10.47: 2 Bond angle restraints: 23020 Sorted by residual: angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.35 5.85 1.30e+00 5.92e-01 2.03e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.66 -6.12 1.36e+00 5.41e-01 2.02e+01 angle pdb=" OE1 GLN E 44 " pdb=" CD GLN E 44 " pdb=" NE2 GLN E 44 " ideal model delta sigma weight residual 122.60 118.53 4.07 1.00e+00 1.00e+00 1.66e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.45 -4.26 1.06e+00 8.90e-01 1.62e+01 angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 113.71 109.96 3.75 9.50e-01 1.11e+00 1.56e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 9640 29.72 - 59.44: 549 59.44 - 89.16: 60 89.16 - 118.89: 3 118.89 - 148.61: 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 -170.24 84.24 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 301.68 153.08 148.61 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 301.68 156.40 145.28 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: 2218 0.093 - 0.186: 209 0.186 - 0.278: 32 0.278 - 0.371: 3 0.371 - 0.464: 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 2.05 0.46 2.00e-01 2.50e+01 5.38e+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 4.68e+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 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.69e-02 3.40e+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 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.046 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP B 623 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 624 " 0.038 2.00e-02 2.50e+03 2.37e-02 9.79e+00 pdb=" CG PHE B 624 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 624 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 624 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 624 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 624 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 624 " 0.023 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 123 2.51 - 3.11: 11991 3.11 - 3.70: 27803 3.70 - 4.30: 42500 4.30 - 4.90: 68512 Nonbonded interactions: 150929 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150924 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 individual isotropic 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.130 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.629 17041 Z= 0.418 Angle : 0.827 13.507 23026 Z= 0.515 Chirality : 0.059 0.464 2464 Planarity : 0.004 0.041 2931 Dihedral : 17.549 148.608 6399 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.34 % Allowed : 16.32 % 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: 0.58 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.32 (0.37), residues: 179 loop : 0.45 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP E 25 HIS 0.006 0.001 HIS C 254 PHE 0.038 0.003 PHE B 624 TYR 0.039 0.002 TYR E 67 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.16748 ( 912) hydrogen bonds : angle 6.70611 ( 2664) SS BOND : bond 0.36318 ( 3) SS BOND : angle 6.07804 ( 6) covalent geometry : bond 0.00607 (17038) covalent geometry : angle 0.82103 (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 651 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 627 time to evaluate : 1.994 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: A 99 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8555 (mmtt) REVERT: A 263 ASP cc_start: 0.8059 (m-30) cc_final: 0.7728 (m-30) REVERT: A 286 ASP cc_start: 0.7667 (m-30) cc_final: 0.7365 (m-30) REVERT: A 362 ASP cc_start: 0.7358 (m-30) cc_final: 0.7047 (m-30) REVERT: A 441 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 604 ARG cc_start: 0.8173 (mmp80) cc_final: 0.7677 (mmp80) REVERT: A 606 TYR cc_start: 0.7135 (m-80) cc_final: 0.6860 (m-10) REVERT: A 632 MET cc_start: 0.8539 (mtt) cc_final: 0.8231 (mtt) REVERT: B 106 LEU cc_start: 0.8744 (tp) cc_final: 0.8537 (tp) REVERT: B 177 ASP cc_start: 0.8434 (t0) cc_final: 0.8208 (t0) REVERT: B 315 ASP cc_start: 0.8448 (p0) cc_final: 0.8196 (p0) REVERT: B 322 MET cc_start: 0.8617 (mmm) cc_final: 0.8410 (mmt) REVERT: B 385 VAL cc_start: 0.8981 (t) cc_final: 0.8568 (t) REVERT: B 586 TYR cc_start: 0.8195 (m-80) cc_final: 0.7894 (m-80) REVERT: B 598 MET cc_start: 0.7634 (mtp) cc_final: 0.7357 (mtp) REVERT: C 137 MET cc_start: 0.3070 (mtp) cc_final: 0.2745 (mtp) outliers start: 24 outliers final: 5 residues processed: 644 average time/residue: 0.3008 time to fit residues: 285.4746 Evaluate side-chains 427 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 421 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 329 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 34 HIS B 180 ASN B 232 ASN B 320 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN D 80 HIS D 132 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108376 restraints weight = 25445.366| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.27 r_work: 0.2958 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17041 Z= 0.166 Angle : 0.619 18.182 23026 Z= 0.320 Chirality : 0.043 0.172 2464 Planarity : 0.004 0.042 2931 Dihedral : 10.527 145.328 2341 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.68 % Allowed : 17.89 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.18), residues: 2012 helix: 1.48 (0.15), residues: 1167 sheet: -0.07 (0.41), residues: 148 loop : 0.45 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 558 HIS 0.006 0.001 HIS B 438 PHE 0.017 0.002 PHE B 492 TYR 0.020 0.002 TYR A 140 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 912) hydrogen bonds : angle 4.90522 ( 2664) SS BOND : bond 0.00228 ( 3) SS BOND : angle 2.37420 ( 6) covalent geometry : bond 0.00367 (17038) covalent geometry : angle 0.61745 (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 490 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 442 time to evaluate : 1.717 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: A 15 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8878 (mt-10) REVERT: A 23 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8844 (mmmm) REVERT: A 49 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8837 (t-90) REVERT: A 65 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7684 (mp0) REVERT: A 209 LYS cc_start: 0.9223 (ttpp) cc_final: 0.8994 (ttmm) REVERT: A 263 ASP cc_start: 0.8903 (m-30) cc_final: 0.8410 (m-30) REVERT: A 286 ASP cc_start: 0.8856 (m-30) cc_final: 0.8231 (m-30) REVERT: A 362 ASP cc_start: 0.8393 (m-30) cc_final: 0.7949 (m-30) REVERT: A 595 MET cc_start: 0.9341 (mmm) cc_final: 0.9085 (mmp) REVERT: A 598 MET cc_start: 0.9295 (mtm) cc_final: 0.9060 (mtp) REVERT: A 599 GLU cc_start: 0.8961 (pt0) cc_final: 0.8684 (pt0) REVERT: A 686 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7972 (ttm-80) REVERT: B 11 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8701 (pt0) REVERT: B 15 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8626 (mm-30) REVERT: B 65 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8201 (mm-30) REVERT: B 104 TYR cc_start: 0.9158 (m-80) cc_final: 0.8647 (m-80) REVERT: B 106 LEU cc_start: 0.9339 (tp) cc_final: 0.9014 (tp) REVERT: B 138 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9156 (mtmm) REVERT: B 150 GLN cc_start: 0.9233 (tp40) cc_final: 0.8633 (tp-100) REVERT: B 158 ASN cc_start: 0.9346 (m-40) cc_final: 0.9113 (m-40) REVERT: B 177 ASP cc_start: 0.8625 (t0) cc_final: 0.8351 (t70) REVERT: B 243 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5365 (ttt180) REVERT: B 266 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8524 (mtpp) REVERT: B 296 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8236 (mmmt) REVERT: B 321 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 322 MET cc_start: 0.9498 (mmm) cc_final: 0.9189 (mmt) REVERT: B 333 LYS cc_start: 0.9305 (tttt) cc_final: 0.8968 (mtpp) REVERT: B 447 ASN cc_start: 0.8618 (m-40) cc_final: 0.8404 (m-40) REVERT: B 452 ARG cc_start: 0.8998 (ttt180) cc_final: 0.8796 (tmm-80) REVERT: B 493 MET cc_start: 0.9663 (tmm) cc_final: 0.9345 (tmm) REVERT: B 515 ASP cc_start: 0.9073 (m-30) cc_final: 0.8641 (m-30) REVERT: B 586 TYR cc_start: 0.9190 (m-80) cc_final: 0.8874 (m-80) REVERT: B 588 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8381 (mm-40) REVERT: B 602 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8282 (tt0) REVERT: B 632 MET cc_start: 0.8779 (mtm) cc_final: 0.8439 (mtm) REVERT: B 686 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8186 (mtp-110) REVERT: C 95 MET cc_start: 0.1016 (ppp) cc_final: 0.0664 (ppp) REVERT: C 130 TYR cc_start: 0.6942 (m-80) cc_final: 0.6648 (m-10) REVERT: C 155 LYS cc_start: 0.4059 (mmtp) cc_final: 0.3464 (ptmt) REVERT: D 91 ASN cc_start: 0.2346 (m-40) cc_final: 0.1707 (t0) REVERT: D 93 MET cc_start: 0.4541 (mmt) cc_final: 0.4331 (mmm) REVERT: D 185 MET cc_start: 0.7177 (mmm) cc_final: 0.6847 (mmm) REVERT: D 189 GLU cc_start: 0.5997 (tt0) cc_final: 0.5535 (pt0) REVERT: E 46 MET cc_start: 0.8488 (tpt) cc_final: 0.8200 (tpt) outliers start: 48 outliers final: 17 residues processed: 474 average time/residue: 0.3175 time to fit residues: 223.7836 Evaluate side-chains 410 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 132 optimal weight: 0.0470 chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 218 ASN A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 645 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 69 GLN D 270 ASN ** E 60 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 = 0.4173 r_free = 0.4173 target = 0.184895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108937 restraints weight = 25504.976| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.09 r_work: 0.2971 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17041 Z= 0.151 Angle : 0.571 14.652 23026 Z= 0.295 Chirality : 0.042 0.171 2464 Planarity : 0.003 0.044 2931 Dihedral : 10.074 140.998 2330 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.91 % Allowed : 16.71 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.19), residues: 2012 helix: 1.69 (0.15), residues: 1163 sheet: 0.08 (0.41), residues: 159 loop : 0.39 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.005 0.001 HIS A 304 PHE 0.017 0.001 PHE C 166 TYR 0.021 0.001 TYR A 140 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 912) hydrogen bonds : angle 4.66161 ( 2664) SS BOND : bond 0.00174 ( 3) SS BOND : angle 2.19480 ( 6) covalent geometry : bond 0.00334 (17038) covalent geometry : angle 0.57024 (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 473 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 421 time to evaluate : 1.848 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: A 23 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8849 (mmmm) REVERT: A 49 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8729 (t-90) REVERT: A 65 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7531 (mp0) REVERT: A 149 TYR cc_start: 0.9290 (t80) cc_final: 0.9043 (t80) REVERT: A 250 TYR cc_start: 0.9292 (m-80) cc_final: 0.8879 (m-80) REVERT: A 263 ASP cc_start: 0.8874 (m-30) cc_final: 0.8308 (m-30) REVERT: A 286 ASP cc_start: 0.8880 (m-30) cc_final: 0.8197 (m-30) REVERT: A 355 TYR cc_start: 0.9283 (m-80) cc_final: 0.9070 (m-80) REVERT: A 362 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: A 458 MET cc_start: 0.9066 (mmm) cc_final: 0.8837 (mmt) REVERT: A 599 GLU cc_start: 0.8956 (pt0) cc_final: 0.8464 (pt0) REVERT: A 602 GLU cc_start: 0.8572 (tt0) cc_final: 0.7871 (tt0) REVERT: A 639 ASP cc_start: 0.9133 (m-30) cc_final: 0.8884 (m-30) REVERT: A 662 MET cc_start: 0.9193 (ptm) cc_final: 0.8948 (ptp) REVERT: B 15 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 21 ASP cc_start: 0.9029 (t0) cc_final: 0.8795 (t0) REVERT: B 43 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8835 (mp10) REVERT: B 65 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8341 (mm-30) REVERT: B 104 TYR cc_start: 0.9125 (m-80) cc_final: 0.8699 (m-80) REVERT: B 106 LEU cc_start: 0.9319 (tp) cc_final: 0.9055 (tp) REVERT: B 147 GLN cc_start: 0.9074 (mt0) cc_final: 0.8760 (mt0) REVERT: B 243 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5378 (ttt180) REVERT: B 266 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8540 (mtpp) REVERT: B 296 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8169 (mmmt) REVERT: B 333 LYS cc_start: 0.9311 (tttt) cc_final: 0.8981 (mtpp) REVERT: B 452 ARG cc_start: 0.9029 (ttt180) cc_final: 0.8827 (tmm-80) REVERT: B 475 ASN cc_start: 0.9446 (m110) cc_final: 0.9045 (m-40) REVERT: B 493 MET cc_start: 0.9639 (tmm) cc_final: 0.9282 (tmm) REVERT: B 586 TYR cc_start: 0.9210 (m-80) cc_final: 0.8869 (m-80) REVERT: B 602 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8145 (tt0) REVERT: B 604 ARG cc_start: 0.9321 (mmm160) cc_final: 0.8816 (mmm160) REVERT: B 662 MET cc_start: 0.8474 (ptp) cc_final: 0.8237 (ptp) REVERT: B 686 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8157 (mtp85) REVERT: C 130 TYR cc_start: 0.6849 (m-80) cc_final: 0.6594 (m-10) REVERT: C 155 LYS cc_start: 0.4174 (mmtp) cc_final: 0.3719 (ptmt) REVERT: C 318 ASP cc_start: 0.9227 (m-30) cc_final: 0.8890 (p0) REVERT: D 91 ASN cc_start: 0.2332 (m-40) cc_final: 0.1751 (t0) REVERT: D 93 MET cc_start: 0.4480 (mmt) cc_final: 0.4253 (mmm) REVERT: D 179 TYR cc_start: 0.6046 (m-10) cc_final: 0.5728 (m-10) REVERT: D 269 MET cc_start: 0.3750 (tpt) cc_final: 0.3151 (mtt) REVERT: E 46 MET cc_start: 0.8654 (tpt) cc_final: 0.8238 (tpt) outliers start: 52 outliers final: 29 residues processed: 453 average time/residue: 0.2896 time to fit residues: 193.9576 Evaluate side-chains 413 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 380 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 197 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 155 optimal weight: 40.0000 chunk 183 optimal weight: 50.0000 chunk 136 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 447 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102602 restraints weight = 26115.735| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.31 r_work: 0.2920 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17041 Z= 0.262 Angle : 0.614 12.839 23026 Z= 0.317 Chirality : 0.044 0.167 2464 Planarity : 0.004 0.045 2931 Dihedral : 10.148 147.448 2330 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.07 % Allowed : 17.61 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2012 helix: 1.68 (0.15), residues: 1170 sheet: -0.04 (0.42), residues: 153 loop : 0.37 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.007 0.001 HIS A 304 PHE 0.017 0.002 PHE B 487 TYR 0.021 0.002 TYR C 22 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 912) hydrogen bonds : angle 4.69648 ( 2664) SS BOND : bond 0.00071 ( 3) SS BOND : angle 3.07890 ( 6) covalent geometry : bond 0.00587 (17038) covalent geometry : angle 0.61233 (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 437 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 382 time to evaluate : 1.723 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: A 23 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (mmmm) REVERT: A 30 LYS cc_start: 0.8923 (tptp) cc_final: 0.8684 (tptt) REVERT: A 49 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8798 (t-90) REVERT: A 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7957 (mp0) REVERT: A 149 TYR cc_start: 0.9314 (t80) cc_final: 0.9088 (t80) REVERT: A 178 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 217 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8923 (mm-30) REVERT: A 250 TYR cc_start: 0.9330 (m-80) cc_final: 0.8766 (m-80) REVERT: A 263 ASP cc_start: 0.8817 (m-30) cc_final: 0.8352 (m-30) REVERT: A 286 ASP cc_start: 0.8921 (m-30) cc_final: 0.8229 (m-30) REVERT: A 362 ASP cc_start: 0.8625 (m-30) cc_final: 0.8117 (m-30) REVERT: A 420 MET cc_start: 0.9449 (mmm) cc_final: 0.9241 (mmm) REVERT: A 570 MET cc_start: 0.8873 (mtp) cc_final: 0.8667 (mtp) REVERT: A 599 GLU cc_start: 0.9020 (pt0) cc_final: 0.8592 (pt0) REVERT: A 602 GLU cc_start: 0.8700 (tt0) cc_final: 0.8032 (tt0) REVERT: A 604 ARG cc_start: 0.8598 (mmp80) cc_final: 0.8383 (mmp80) REVERT: B 15 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8681 (mm-30) REVERT: B 43 GLN cc_start: 0.9382 (mm-40) cc_final: 0.8925 (mp10) REVERT: B 66 GLU cc_start: 0.8464 (tp30) cc_final: 0.8240 (tp30) REVERT: B 104 TYR cc_start: 0.9280 (m-80) cc_final: 0.8948 (m-80) REVERT: B 106 LEU cc_start: 0.9348 (tp) cc_final: 0.9053 (tp) REVERT: B 177 ASP cc_start: 0.8715 (t0) cc_final: 0.8497 (t70) REVERT: B 296 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8400 (mmmt) REVERT: B 333 LYS cc_start: 0.9365 (tttt) cc_final: 0.9022 (mtpp) REVERT: B 402 GLU cc_start: 0.8844 (mp0) cc_final: 0.8485 (mp0) REVERT: B 452 ARG cc_start: 0.9111 (ttt180) cc_final: 0.8852 (tmm-80) REVERT: B 471 TYR cc_start: 0.9462 (t80) cc_final: 0.9215 (t80) REVERT: B 475 ASN cc_start: 0.9458 (m110) cc_final: 0.9111 (m-40) REVERT: B 493 MET cc_start: 0.9670 (tmm) cc_final: 0.9390 (tmm) REVERT: B 515 ASP cc_start: 0.9043 (m-30) cc_final: 0.8794 (m-30) REVERT: B 586 TYR cc_start: 0.9260 (m-80) cc_final: 0.8811 (m-80) REVERT: B 588 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8481 (mm-40) REVERT: B 602 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8016 (tt0) REVERT: B 615 MET cc_start: 0.9634 (mmp) cc_final: 0.9213 (mmp) REVERT: B 684 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: C 95 MET cc_start: 0.1132 (ppp) cc_final: 0.0930 (ppp) REVERT: C 130 TYR cc_start: 0.6927 (m-80) cc_final: 0.6682 (m-10) REVERT: C 155 LYS cc_start: 0.4292 (mmtp) cc_final: 0.3809 (ptmt) REVERT: C 318 ASP cc_start: 0.9212 (m-30) cc_final: 0.8976 (p0) REVERT: D 91 ASN cc_start: 0.2501 (m-40) cc_final: 0.2050 (t0) REVERT: D 269 MET cc_start: 0.3328 (tpt) cc_final: 0.2852 (mpp) REVERT: E 46 MET cc_start: 0.8690 (tpt) cc_final: 0.8246 (tpt) outliers start: 55 outliers final: 37 residues processed: 415 average time/residue: 0.2832 time to fit residues: 176.9201 Evaluate side-chains 401 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 645 GLN B 447 ASN B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109376 restraints weight = 26263.892| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.43 r_work: 0.2933 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17041 Z= 0.126 Angle : 0.555 16.910 23026 Z= 0.284 Chirality : 0.041 0.180 2464 Planarity : 0.003 0.046 2931 Dihedral : 9.814 141.808 2326 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 19.34 % Favored : 78.42 % 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: 1.53 (0.19), residues: 2012 helix: 1.73 (0.15), residues: 1183 sheet: -0.34 (0.42), residues: 157 loop : 0.19 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 558 HIS 0.004 0.001 HIS B 438 PHE 0.018 0.001 PHE A 492 TYR 0.025 0.001 TYR D 105 ARG 0.006 0.000 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 912) hydrogen bonds : angle 4.52933 ( 2664) SS BOND : bond 0.00293 ( 3) SS BOND : angle 2.54767 ( 6) covalent geometry : bond 0.00280 (17038) covalent geometry : angle 0.55319 (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 452 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 412 time to evaluate : 1.864 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: A 23 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8836 (mmmm) REVERT: A 29 ASP cc_start: 0.9239 (t0) cc_final: 0.8898 (t70) REVERT: A 49 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8923 (t-90) REVERT: A 65 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7645 (mp0) REVERT: A 136 LYS cc_start: 0.9270 (tptt) cc_final: 0.9060 (tptp) REVERT: A 217 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8891 (mm-30) REVERT: A 250 TYR cc_start: 0.9306 (m-80) cc_final: 0.8972 (m-80) REVERT: A 263 ASP cc_start: 0.8739 (m-30) cc_final: 0.8365 (m-30) REVERT: A 274 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8261 (ttm170) REVERT: A 286 ASP cc_start: 0.8958 (m-30) cc_final: 0.8212 (m-30) REVERT: A 362 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 420 MET cc_start: 0.9523 (mmm) cc_final: 0.9283 (mmm) REVERT: A 599 GLU cc_start: 0.8929 (pt0) cc_final: 0.8348 (pt0) REVERT: A 602 GLU cc_start: 0.8727 (tt0) cc_final: 0.8250 (tt0) REVERT: A 604 ARG cc_start: 0.8374 (mmp80) cc_final: 0.8099 (mmp80) REVERT: A 686 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7771 (mmm-85) REVERT: B 15 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 43 GLN cc_start: 0.9443 (mm-40) cc_final: 0.8988 (mp10) REVERT: B 44 ASN cc_start: 0.9280 (m110) cc_final: 0.8855 (m-40) REVERT: B 66 GLU cc_start: 0.8445 (tp30) cc_final: 0.8148 (tp30) REVERT: B 104 TYR cc_start: 0.9168 (m-80) cc_final: 0.8911 (m-80) REVERT: B 106 LEU cc_start: 0.9345 (tp) cc_final: 0.9073 (tp) REVERT: B 147 GLN cc_start: 0.9162 (mt0) cc_final: 0.8829 (mt0) REVERT: B 157 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8696 (mp) REVERT: B 228 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8993 (mmtt) REVERT: B 296 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8467 (mmmt) REVERT: B 333 LYS cc_start: 0.9234 (tttt) cc_final: 0.8937 (mtpp) REVERT: B 402 GLU cc_start: 0.8879 (mp0) cc_final: 0.8576 (mp0) REVERT: B 446 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8200 (mmm-85) REVERT: B 452 ARG cc_start: 0.8919 (ttt180) cc_final: 0.8630 (tmm-80) REVERT: B 475 ASN cc_start: 0.9478 (m110) cc_final: 0.9096 (m-40) REVERT: B 586 TYR cc_start: 0.9165 (m-80) cc_final: 0.8808 (m-80) REVERT: B 602 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8150 (tt0) REVERT: B 610 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8945 (mtmm) REVERT: B 662 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (ptp) REVERT: B 686 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7889 (mtp-110) REVERT: C 96 MET cc_start: 0.0417 (mmt) cc_final: 0.0176 (mmt) REVERT: C 130 TYR cc_start: 0.6955 (m-80) cc_final: 0.6710 (m-10) REVERT: C 155 LYS cc_start: 0.4338 (mmtp) cc_final: 0.3949 (ptmt) REVERT: C 318 ASP cc_start: 0.9321 (m-30) cc_final: 0.9014 (p0) REVERT: D 91 ASN cc_start: 0.2416 (m-40) cc_final: 0.1897 (t0) REVERT: D 93 MET cc_start: 0.3758 (mmt) cc_final: 0.3468 (mmm) REVERT: D 269 MET cc_start: 0.3897 (tpt) cc_final: 0.3428 (mpp) REVERT: E 46 MET cc_start: 0.8692 (tpt) cc_final: 0.8226 (tpt) outliers start: 40 outliers final: 26 residues processed: 431 average time/residue: 0.2884 time to fit residues: 185.7186 Evaluate side-chains 413 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 382 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 186 optimal weight: 50.0000 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 180 ASN B 320 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.183244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104208 restraints weight = 26841.131| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.20 r_work: 0.2884 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17041 Z= 0.244 Angle : 0.618 15.908 23026 Z= 0.315 Chirality : 0.044 0.164 2464 Planarity : 0.004 0.042 2931 Dihedral : 9.924 149.584 2326 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.13 % Allowed : 19.01 % Favored : 77.86 % 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: 1.47 (0.19), residues: 2012 helix: 1.69 (0.15), residues: 1186 sheet: -0.45 (0.41), residues: 157 loop : 0.17 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 44 HIS 0.006 0.001 HIS A 304 PHE 0.026 0.002 PHE C 227 TYR 0.021 0.002 TYR D 179 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 912) hydrogen bonds : angle 4.61263 ( 2664) SS BOND : bond 0.00233 ( 3) SS BOND : angle 2.81816 ( 6) covalent geometry : bond 0.00548 (17038) covalent geometry : angle 0.61635 (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 428 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (mmmm) REVERT: A 29 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8951 (t70) REVERT: A 30 LYS cc_start: 0.8915 (tptp) cc_final: 0.8616 (tptt) REVERT: A 49 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8852 (t-90) REVERT: A 65 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7867 (mp0) REVERT: A 136 LYS cc_start: 0.9292 (tptt) cc_final: 0.9068 (tptp) REVERT: A 217 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8970 (mm-30) REVERT: A 250 TYR cc_start: 0.9360 (m-80) cc_final: 0.8832 (m-80) REVERT: A 263 ASP cc_start: 0.8829 (m-30) cc_final: 0.8434 (m-30) REVERT: A 274 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8402 (ttm170) REVERT: A 286 ASP cc_start: 0.8922 (m-30) cc_final: 0.8222 (m-30) REVERT: A 290 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 317 MET cc_start: 0.9090 (mtp) cc_final: 0.8867 (mtt) REVERT: A 362 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: A 420 MET cc_start: 0.9468 (mmm) cc_final: 0.9216 (mmm) REVERT: A 599 GLU cc_start: 0.8991 (pt0) cc_final: 0.8468 (pt0) REVERT: A 602 GLU cc_start: 0.8543 (tt0) cc_final: 0.8184 (tt0) REVERT: B 15 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8706 (mm-30) REVERT: B 43 GLN cc_start: 0.9423 (mm-40) cc_final: 0.9017 (mp10) REVERT: B 44 ASN cc_start: 0.9292 (m110) cc_final: 0.8831 (m-40) REVERT: B 66 GLU cc_start: 0.8413 (tp30) cc_final: 0.8052 (tp30) REVERT: B 106 LEU cc_start: 0.9374 (tp) cc_final: 0.9068 (tp) REVERT: B 177 ASP cc_start: 0.8717 (t0) cc_final: 0.8490 (t70) REVERT: B 235 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8903 (ttm110) REVERT: B 274 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8039 (ttm170) REVERT: B 296 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8483 (mmmt) REVERT: B 333 LYS cc_start: 0.9331 (tttt) cc_final: 0.9006 (mtpp) REVERT: B 402 GLU cc_start: 0.8959 (mp0) cc_final: 0.8635 (mp0) REVERT: B 446 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8287 (mmm-85) REVERT: B 452 ARG cc_start: 0.9086 (ttt180) cc_final: 0.8751 (tmm-80) REVERT: B 475 ASN cc_start: 0.9458 (m110) cc_final: 0.9039 (m-40) REVERT: B 586 TYR cc_start: 0.9261 (m-80) cc_final: 0.8877 (m-80) REVERT: B 588 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 602 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8091 (tt0) REVERT: B 610 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8854 (mtmm) REVERT: B 662 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8064 (mtm) REVERT: B 684 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: C 155 LYS cc_start: 0.4758 (mmtp) cc_final: 0.4557 (ptmt) REVERT: C 318 ASP cc_start: 0.9244 (m-30) cc_final: 0.8981 (p0) REVERT: D 91 ASN cc_start: 0.2383 (m-40) cc_final: 0.2052 (t0) REVERT: D 269 MET cc_start: 0.4049 (tpt) cc_final: 0.3631 (mpp) REVERT: D 270 ASN cc_start: 0.3712 (m110) cc_final: 0.3086 (t0) REVERT: E 46 MET cc_start: 0.8625 (tpt) cc_final: 0.8114 (tpt) REVERT: E 70 MET cc_start: 0.7634 (mtt) cc_final: 0.6422 (mpp) outliers start: 56 outliers final: 35 residues processed: 407 average time/residue: 0.2773 time to fit residues: 168.8830 Evaluate side-chains 397 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 355 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 560 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 218 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108080 restraints weight = 26214.622| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.25 r_work: 0.2929 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17041 Z= 0.136 Angle : 0.587 14.500 23026 Z= 0.298 Chirality : 0.042 0.249 2464 Planarity : 0.003 0.045 2931 Dihedral : 9.667 144.216 2326 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.52 % Allowed : 19.73 % Favored : 77.75 % 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: 1.34 (0.19), residues: 2012 helix: 1.60 (0.15), residues: 1197 sheet: -0.48 (0.42), residues: 157 loop : 0.06 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.005 0.001 HIS C 201 PHE 0.036 0.001 PHE C 227 TYR 0.030 0.001 TYR D 105 ARG 0.006 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 912) hydrogen bonds : angle 4.59524 ( 2664) SS BOND : bond 0.00239 ( 3) SS BOND : angle 2.34171 ( 6) covalent geometry : bond 0.00302 (17038) covalent geometry : angle 0.58585 (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 442 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 397 time to evaluate : 1.793 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: A 23 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8838 (mmmm) REVERT: A 29 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8884 (t70) REVERT: A 30 LYS cc_start: 0.8890 (tptp) cc_final: 0.8574 (tptt) REVERT: A 49 HIS cc_start: 0.9249 (OUTLIER) cc_final: 0.8925 (t-90) REVERT: A 65 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7627 (mp0) REVERT: A 217 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8980 (mm-30) REVERT: A 250 TYR cc_start: 0.9326 (m-80) cc_final: 0.8949 (m-80) REVERT: A 263 ASP cc_start: 0.8761 (m-30) cc_final: 0.8368 (m-30) REVERT: A 274 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8274 (ttm170) REVERT: A 276 LYS cc_start: 0.9252 (tppt) cc_final: 0.9023 (mmtm) REVERT: A 286 ASP cc_start: 0.8958 (m-30) cc_final: 0.8176 (m-30) REVERT: A 290 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8259 (tm-30) REVERT: A 317 MET cc_start: 0.8976 (mtp) cc_final: 0.8656 (mtt) REVERT: A 362 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 420 MET cc_start: 0.9488 (mmm) cc_final: 0.9242 (mmm) REVERT: A 509 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8955 (tm-30) REVERT: A 599 GLU cc_start: 0.8923 (pt0) cc_final: 0.8298 (pt0) REVERT: A 602 GLU cc_start: 0.8666 (tt0) cc_final: 0.7833 (tt0) REVERT: B 15 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 43 GLN cc_start: 0.9449 (mm-40) cc_final: 0.9001 (mp10) REVERT: B 44 ASN cc_start: 0.9274 (m110) cc_final: 0.8837 (m-40) REVERT: B 65 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8124 (mp0) REVERT: B 66 GLU cc_start: 0.8421 (tp30) cc_final: 0.7955 (tp30) REVERT: B 106 LEU cc_start: 0.9357 (tp) cc_final: 0.9077 (tp) REVERT: B 147 GLN cc_start: 0.9246 (mt0) cc_final: 0.8871 (mt0) REVERT: B 235 ARG cc_start: 0.9191 (ttm-80) cc_final: 0.8889 (ttm110) REVERT: B 274 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7992 (ttm170) REVERT: B 296 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8540 (mmmt) REVERT: B 333 LYS cc_start: 0.9239 (tttt) cc_final: 0.8941 (mtpp) REVERT: B 402 GLU cc_start: 0.8922 (mp0) cc_final: 0.8581 (mp0) REVERT: B 415 ASN cc_start: 0.9378 (t0) cc_final: 0.8899 (t0) REVERT: B 446 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: B 452 ARG cc_start: 0.8912 (ttt180) cc_final: 0.8584 (tmm-80) REVERT: B 475 ASN cc_start: 0.9487 (m110) cc_final: 0.9092 (m-40) REVERT: B 586 TYR cc_start: 0.9180 (m-80) cc_final: 0.8882 (m-80) REVERT: B 602 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8211 (tt0) REVERT: B 610 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8897 (mtmm) REVERT: B 662 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: B 684 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: C 109 PHE cc_start: 0.5484 (m-10) cc_final: 0.5165 (m-10) REVERT: C 318 ASP cc_start: 0.9343 (m-30) cc_final: 0.9039 (p0) REVERT: D 91 ASN cc_start: 0.1756 (m-40) cc_final: 0.1302 (t0) REVERT: D 269 MET cc_start: 0.4047 (tpt) cc_final: 0.3681 (mpp) REVERT: D 270 ASN cc_start: 0.4045 (m110) cc_final: 0.3426 (t0) REVERT: E 46 MET cc_start: 0.8555 (tpt) cc_final: 0.8031 (tpt) outliers start: 45 outliers final: 23 residues processed: 423 average time/residue: 0.2889 time to fit residues: 180.8293 Evaluate side-chains 401 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 371 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 139 optimal weight: 8.9990 chunk 44 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 218 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.186220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108724 restraints weight = 26093.849| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.25 r_work: 0.2947 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17041 Z= 0.148 Angle : 0.608 15.952 23026 Z= 0.310 Chirality : 0.043 0.295 2464 Planarity : 0.003 0.041 2931 Dihedral : 9.526 143.257 2325 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.40 % Allowed : 20.63 % Favored : 76.97 % 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 (0.19), residues: 2012 helix: 1.50 (0.15), residues: 1192 sheet: -0.48 (0.43), residues: 157 loop : -0.01 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 30 HIS 0.004 0.001 HIS A 304 PHE 0.033 0.001 PHE C 227 TYR 0.084 0.002 TYR D 179 ARG 0.005 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 912) hydrogen bonds : angle 4.62539 ( 2664) SS BOND : bond 0.00632 ( 3) SS BOND : angle 2.36498 ( 6) covalent geometry : bond 0.00338 (17038) covalent geometry : angle 0.60676 (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 430 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 387 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (mmmm) REVERT: A 29 ASP cc_start: 0.9242 (OUTLIER) cc_final: 0.8875 (t70) REVERT: A 30 LYS cc_start: 0.8792 (tptp) cc_final: 0.8524 (tptt) REVERT: A 49 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8862 (t-90) REVERT: A 65 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7632 (mp0) REVERT: A 217 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9027 (mm-30) REVERT: A 250 TYR cc_start: 0.9332 (m-80) cc_final: 0.8951 (m-80) REVERT: A 274 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8306 (ttm170) REVERT: A 286 ASP cc_start: 0.8811 (m-30) cc_final: 0.8111 (m-30) REVERT: A 290 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 316 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 317 MET cc_start: 0.8912 (mtp) cc_final: 0.8654 (mtp) REVERT: A 362 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: A 394 TYR cc_start: 0.9323 (m-80) cc_final: 0.9083 (m-80) REVERT: A 420 MET cc_start: 0.9492 (mmm) cc_final: 0.9231 (mmm) REVERT: A 509 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8937 (tm-30) REVERT: A 599 GLU cc_start: 0.8975 (pt0) cc_final: 0.8604 (pt0) REVERT: A 602 GLU cc_start: 0.8597 (tt0) cc_final: 0.7432 (tt0) REVERT: A 604 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7475 (mmt-90) REVERT: B 15 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8680 (mm-30) REVERT: B 43 GLN cc_start: 0.9401 (mm-40) cc_final: 0.8973 (mp10) REVERT: B 44 ASN cc_start: 0.9247 (m110) cc_final: 0.8826 (m-40) REVERT: B 65 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8120 (mp0) REVERT: B 66 GLU cc_start: 0.8405 (tp30) cc_final: 0.7925 (tp30) REVERT: B 106 LEU cc_start: 0.9376 (tp) cc_final: 0.9106 (tp) REVERT: B 235 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8782 (ttm110) REVERT: B 274 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8034 (ttm170) REVERT: B 296 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8512 (mmmt) REVERT: B 333 LYS cc_start: 0.9241 (tttt) cc_final: 0.8929 (mtpp) REVERT: B 357 TYR cc_start: 0.9316 (m-10) cc_final: 0.8569 (m-80) REVERT: B 402 GLU cc_start: 0.8931 (mp0) cc_final: 0.8637 (mp0) REVERT: B 415 ASN cc_start: 0.9358 (t0) cc_final: 0.8957 (t0) REVERT: B 446 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8014 (tpp80) REVERT: B 452 ARG cc_start: 0.8964 (ttt180) cc_final: 0.8673 (tmm-80) REVERT: B 475 ASN cc_start: 0.9450 (m110) cc_final: 0.9049 (m-40) REVERT: B 586 TYR cc_start: 0.9136 (m-80) cc_final: 0.8868 (m-80) REVERT: B 602 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8150 (tt0) REVERT: B 610 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8919 (mtmm) REVERT: B 615 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.9166 (mmp) REVERT: B 662 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7955 (mtm) REVERT: B 684 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7214 (m-10) REVERT: B 686 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.8138 (mtp-110) REVERT: C 318 ASP cc_start: 0.9267 (m-30) cc_final: 0.9015 (p0) REVERT: D 91 ASN cc_start: 0.1397 (m-40) cc_final: 0.0893 (t0) REVERT: D 269 MET cc_start: 0.4107 (tpt) cc_final: 0.3732 (mpp) REVERT: D 270 ASN cc_start: 0.3782 (m110) cc_final: 0.3198 (t0) REVERT: E 34 MET cc_start: 0.8370 (ppp) cc_final: 0.8090 (ppp) REVERT: E 46 MET cc_start: 0.8579 (tpt) cc_final: 0.8056 (tpt) outliers start: 43 outliers final: 27 residues processed: 411 average time/residue: 0.2927 time to fit residues: 177.5219 Evaluate side-chains 399 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 184 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110958 restraints weight = 26297.438| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.39 r_work: 0.2976 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17041 Z= 0.136 Angle : 0.620 12.373 23026 Z= 0.315 Chirality : 0.043 0.292 2464 Planarity : 0.003 0.042 2931 Dihedral : 9.304 141.565 2325 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.24 % Allowed : 21.35 % Favored : 76.41 % 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: 1.12 (0.18), residues: 2012 helix: 1.38 (0.15), residues: 1194 sheet: 0.16 (0.53), residues: 103 loop : -0.13 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 30 HIS 0.005 0.001 HIS D 101 PHE 0.044 0.001 PHE C 109 TYR 0.022 0.001 TYR D 179 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 912) hydrogen bonds : angle 4.62201 ( 2664) SS BOND : bond 0.00242 ( 3) SS BOND : angle 2.13983 ( 6) covalent geometry : bond 0.00309 (17038) covalent geometry : angle 0.61905 (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 423 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 383 time to evaluate : 1.731 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: A 23 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8776 (mmmm) REVERT: A 29 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.8874 (t70) REVERT: A 30 LYS cc_start: 0.8783 (tptp) cc_final: 0.8501 (tptt) REVERT: A 56 ASP cc_start: 0.9027 (m-30) cc_final: 0.8781 (m-30) REVERT: A 65 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7557 (mp0) REVERT: A 250 TYR cc_start: 0.9306 (m-80) cc_final: 0.8945 (m-80) REVERT: A 276 LYS cc_start: 0.9308 (tppt) cc_final: 0.8975 (tppt) REVERT: A 286 ASP cc_start: 0.8823 (m-30) cc_final: 0.8111 (m-30) REVERT: A 316 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 317 MET cc_start: 0.8943 (mtp) cc_final: 0.8608 (mtp) REVERT: A 362 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: A 394 TYR cc_start: 0.9289 (m-80) cc_final: 0.9068 (m-80) REVERT: A 420 MET cc_start: 0.9475 (mmm) cc_final: 0.9170 (mmm) REVERT: A 471 TYR cc_start: 0.9167 (t80) cc_final: 0.8942 (t80) REVERT: A 509 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8921 (tm-30) REVERT: A 599 GLU cc_start: 0.8987 (pt0) cc_final: 0.8702 (pt0) REVERT: A 602 GLU cc_start: 0.8572 (tt0) cc_final: 0.7348 (tt0) REVERT: A 604 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7559 (mmt-90) REVERT: B 15 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8684 (mm-30) REVERT: B 43 GLN cc_start: 0.9409 (mm-40) cc_final: 0.8979 (mp10) REVERT: B 44 ASN cc_start: 0.9230 (m110) cc_final: 0.8806 (m-40) REVERT: B 65 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8047 (mp0) REVERT: B 66 GLU cc_start: 0.8390 (tp30) cc_final: 0.7883 (tp30) REVERT: B 235 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8775 (ttm110) REVERT: B 274 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8426 (ttm-80) REVERT: B 296 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8513 (mmmt) REVERT: B 333 LYS cc_start: 0.9269 (tttt) cc_final: 0.8962 (mtpp) REVERT: B 357 TYR cc_start: 0.9284 (m-10) cc_final: 0.8536 (m-80) REVERT: B 402 GLU cc_start: 0.8946 (mp0) cc_final: 0.8616 (mp0) REVERT: B 415 ASN cc_start: 0.9333 (t0) cc_final: 0.8950 (t0) REVERT: B 452 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8603 (tmm-80) REVERT: B 475 ASN cc_start: 0.9454 (m110) cc_final: 0.9017 (m-40) REVERT: B 570 MET cc_start: 0.8825 (ttp) cc_final: 0.8610 (ttm) REVERT: B 602 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8283 (tt0) REVERT: B 610 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8949 (mtmm) REVERT: B 615 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.9166 (mmp) REVERT: B 628 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8394 (mm-30) REVERT: B 662 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (mtm) REVERT: B 684 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: B 686 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8181 (mtp-110) REVERT: C 109 PHE cc_start: 0.4779 (m-10) cc_final: 0.4442 (m-10) REVERT: C 110 MET cc_start: 0.5371 (mpp) cc_final: 0.5001 (pmm) REVERT: C 157 MET cc_start: 0.3102 (tpp) cc_final: 0.2858 (tpp) REVERT: C 269 MET cc_start: 0.6042 (tpp) cc_final: 0.5613 (ptt) REVERT: C 318 ASP cc_start: 0.9255 (m-30) cc_final: 0.8991 (p0) REVERT: D 33 GLU cc_start: 0.4407 (mp0) cc_final: 0.3442 (pt0) REVERT: D 91 ASN cc_start: 0.1482 (m-40) cc_final: 0.1090 (t0) REVERT: D 137 MET cc_start: 0.3400 (tpt) cc_final: 0.2884 (mtm) REVERT: D 269 MET cc_start: 0.4257 (tpt) cc_final: 0.3896 (mtp) REVERT: D 270 ASN cc_start: 0.3872 (m110) cc_final: 0.3223 (t0) REVERT: E 34 MET cc_start: 0.8464 (ppp) cc_final: 0.8246 (ppp) REVERT: E 46 MET cc_start: 0.8607 (tpt) cc_final: 0.8067 (tpt) outliers start: 40 outliers final: 28 residues processed: 405 average time/residue: 0.2922 time to fit residues: 175.7436 Evaluate side-chains 403 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.189681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113420 restraints weight = 26427.654| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.46 r_work: 0.2975 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17041 Z= 0.146 Angle : 0.646 12.736 23026 Z= 0.327 Chirality : 0.044 0.291 2464 Planarity : 0.004 0.048 2931 Dihedral : 9.243 141.737 2325 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.18 % Allowed : 21.69 % Favored : 76.13 % 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: 1.06 (0.18), residues: 2012 helix: 1.32 (0.15), residues: 1198 sheet: 0.22 (0.53), residues: 103 loop : -0.14 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 30 HIS 0.006 0.001 HIS D 201 PHE 0.039 0.002 PHE C 109 TYR 0.036 0.001 TYR D 142 ARG 0.008 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 912) hydrogen bonds : angle 4.61625 ( 2664) SS BOND : bond 0.00143 ( 3) SS BOND : angle 2.36994 ( 6) covalent geometry : bond 0.00333 (17038) covalent geometry : angle 0.64501 (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 406 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 367 time to evaluate : 1.833 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: A 29 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8881 (t70) REVERT: A 56 ASP cc_start: 0.9025 (m-30) cc_final: 0.8786 (m-30) REVERT: A 65 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7592 (mp0) REVERT: A 250 TYR cc_start: 0.9314 (m-80) cc_final: 0.8900 (m-80) REVERT: A 274 ARG cc_start: 0.8642 (ttm170) cc_final: 0.8405 (ttm170) REVERT: A 286 ASP cc_start: 0.8807 (m-30) cc_final: 0.8101 (m-30) REVERT: A 290 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 316 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 317 MET cc_start: 0.9057 (mtp) cc_final: 0.8686 (mtt) REVERT: A 362 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: A 394 TYR cc_start: 0.9294 (m-80) cc_final: 0.9093 (m-80) REVERT: A 420 MET cc_start: 0.9470 (mmm) cc_final: 0.9210 (mmm) REVERT: A 509 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8938 (tm-30) REVERT: A 602 GLU cc_start: 0.8538 (tt0) cc_final: 0.7456 (tt0) REVERT: A 604 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7533 (mmt-90) REVERT: B 15 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8663 (mm-30) REVERT: B 43 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8970 (mp10) REVERT: B 44 ASN cc_start: 0.9224 (m110) cc_final: 0.8801 (m-40) REVERT: B 65 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8055 (mp0) REVERT: B 66 GLU cc_start: 0.8388 (tp30) cc_final: 0.7873 (tp30) REVERT: B 106 LEU cc_start: 0.9305 (tp) cc_final: 0.9104 (tp) REVERT: B 235 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8725 (ttm110) REVERT: B 274 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8395 (ttm-80) REVERT: B 333 LYS cc_start: 0.9280 (tttt) cc_final: 0.8965 (mtpp) REVERT: B 357 TYR cc_start: 0.9299 (m-10) cc_final: 0.8528 (m-80) REVERT: B 402 GLU cc_start: 0.8933 (mp0) cc_final: 0.8641 (mp0) REVERT: B 415 ASN cc_start: 0.9357 (t0) cc_final: 0.9005 (t0) REVERT: B 452 ARG cc_start: 0.8908 (ttt180) cc_final: 0.8694 (tmm-80) REVERT: B 475 ASN cc_start: 0.9452 (m110) cc_final: 0.9035 (m-40) REVERT: B 570 MET cc_start: 0.8814 (ttm) cc_final: 0.8576 (ttm) REVERT: B 602 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8809 (tt0) REVERT: B 604 ARG cc_start: 0.9243 (mmm160) cc_final: 0.8873 (mmm160) REVERT: B 610 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8950 (mtmm) REVERT: B 615 MET cc_start: 0.9627 (OUTLIER) cc_final: 0.9195 (mmp) REVERT: B 628 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8379 (mm-30) REVERT: B 662 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7845 (mtm) REVERT: B 684 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: B 686 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8217 (mtp-110) REVERT: C 50 ASN cc_start: 0.5683 (p0) cc_final: 0.5375 (m-40) REVERT: C 110 MET cc_start: 0.5367 (mpp) cc_final: 0.4975 (pmm) REVERT: C 269 MET cc_start: 0.6042 (tpp) cc_final: 0.5589 (ptt) REVERT: C 318 ASP cc_start: 0.9213 (m-30) cc_final: 0.8945 (p0) REVERT: D 33 GLU cc_start: 0.4764 (mp0) cc_final: 0.4050 (pt0) REVERT: D 91 ASN cc_start: 0.1199 (m-40) cc_final: 0.0760 (t0) REVERT: D 137 MET cc_start: 0.3496 (tpt) cc_final: 0.2979 (mtm) REVERT: D 269 MET cc_start: 0.4183 (tpt) cc_final: 0.3760 (mtp) REVERT: E 46 MET cc_start: 0.8535 (tpt) cc_final: 0.8011 (tpt) outliers start: 39 outliers final: 29 residues processed: 387 average time/residue: 0.2931 time to fit residues: 169.6313 Evaluate side-chains 388 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 THR 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: 4.9990 chunk 198 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 232 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 127 GLN ** 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 = 0.4116 r_free = 0.4116 target = 0.184797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107861 restraints weight = 26465.042| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.35 r_work: 0.2899 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17041 Z= 0.233 Angle : 0.679 13.752 23026 Z= 0.347 Chirality : 0.046 0.353 2464 Planarity : 0.004 0.050 2931 Dihedral : 9.382 146.800 2325 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 21.52 % Favored : 75.80 % 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: 0.94 (0.18), residues: 2012 helix: 1.24 (0.15), residues: 1196 sheet: -0.55 (0.43), residues: 157 loop : -0.04 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.005 0.001 HIS D 101 PHE 0.035 0.002 PHE C 109 TYR 0.025 0.002 TYR B 471 ARG 0.009 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 912) hydrogen bonds : angle 4.71294 ( 2664) SS BOND : bond 0.00382 ( 3) SS BOND : angle 2.90708 ( 6) covalent geometry : bond 0.00528 (17038) covalent geometry : angle 0.67743 (23020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11157.41 seconds wall clock time: 193 minutes 0.65 seconds (11580.65 seconds total)