Starting phenix.real_space_refine on Fri Jul 3 04:31:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxt_45011/07_2026/9bxt_45011.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 7715 2.51 5 N 2002 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12164 Number of models: 1 Model: "" Number of chains: 7 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} 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} Time building chain proxies: 2.76, per 1000 atoms: 0.23 Number of scatterers: 12164 At special positions: 0 Unit cell: (90.246, 92.274, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 16 15.00 Mg 2 11.99 O 2364 8.00 N 2002 7.00 C 7715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 532.5 milliseconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 11 sheets defined 53.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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: 4.259A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.787A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.231A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.568A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.103A 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: 3.612A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.633A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.880A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.513A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.563A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.255A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.811A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.017A 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: 7.539A 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: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.515A 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: 6.817A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.468A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1602 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: 1.97 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3862 1.34 - 1.46: 2298 1.46 - 1.58: 6122 1.58 - 1.70: 26 1.70 - 1.82: 120 Bond restraints: 12428 Sorted by residual: bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " ideal model delta sigma weight residual 1.748 1.612 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O3A TTP B 802 " pdb=" PB TTP B 802 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C4 TTP B 802 " pdb=" N3 TTP B 802 " ideal model delta sigma weight residual 1.385 1.334 0.051 2.00e-02 2.50e+03 6.58e+00 ... (remaining 12423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 16395 2.08 - 4.15: 315 4.15 - 6.23: 62 6.23 - 8.30: 12 8.30 - 10.38: 6 Bond angle restraints: 16790 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 131.20 125.33 5.87 1.30e+00 5.92e-01 2.04e+01 angle pdb=" OE1 GLN E 44 " pdb=" CD GLN E 44 " pdb=" NE2 GLN E 44 " ideal model delta sigma weight residual 122.60 118.51 4.09 1.00e+00 1.00e+00 1.67e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.47 -4.28 1.06e+00 8.90e-01 1.63e+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 angle pdb=" CA ASP E 43 " pdb=" CB ASP E 43 " pdb=" CG ASP E 43 " ideal model delta sigma weight residual 112.60 108.97 3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 16785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 6881 26.14 - 52.29: 596 52.29 - 78.43: 81 78.43 - 104.58: 8 104.58 - 130.72: 2 Dihedral angle restraints: 7568 sinusoidal: 3198 harmonic: 4370 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 -170.22 84.22 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" O4' GDP A 804 " pdb=" C1' GDP A 804 " pdb=" N9 GDP A 804 " pdb=" C8 GDP A 804 " ideal model delta sinusoidal sigma weight residual 27.02 -103.70 130.72 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -101.10 128.12 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 7565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1272 0.040 - 0.081: 382 0.081 - 0.121: 118 0.121 - 0.162: 17 0.162 - 0.202: 5 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CA PRO E 31 " pdb=" N PRO E 31 " pdb=" C PRO E 31 " pdb=" CB PRO E 31 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU E 99 " pdb=" CB LEU E 99 " pdb=" CD1 LEU E 99 " pdb=" CD2 LEU E 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU E 21 " pdb=" CB LEU E 21 " pdb=" CD1 LEU E 21 " pdb=" CD2 LEU E 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 1791 not shown) Planarity restraints: 2131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.078 2.00e-02 2.50e+03 3.71e-02 3.44e+01 pdb=" CG TRP E 25 " -0.021 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 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 28 " -0.027 2.00e-02 2.50e+03 1.57e-02 6.20e+00 pdb=" CG TRP E 28 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP E 28 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 28 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP E 28 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP E 28 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 28 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 28 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 28 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 28 " -0.009 2.00e-02 2.50e+03 ... (remaining 2128 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 272 2.67 - 3.23: 11695 3.23 - 3.79: 21538 3.79 - 4.34: 30329 4.34 - 4.90: 48552 Nonbonded interactions: 112386 Sorted by model distance: nonbonded pdb=" O2A TTP A 801 " pdb="MG MG A 802 " model vdw 2.118 2.170 nonbonded pdb=" O PRO B 616 " pdb=" OH TYR B 626 " model vdw 2.132 3.040 nonbonded pdb=" O PRO A 616 " pdb=" OH TYR A 626 " model vdw 2.153 3.040 nonbonded pdb=" O GLU A 119 " pdb=" OG SER A 123 " model vdw 2.175 3.040 nonbonded pdb=" NE2 HIS A 372 " pdb=" O GLN A 516 " model vdw 2.202 3.120 ... (remaining 112381 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=1.00 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.007 0.630 12431 Z= 0.364 Angle : 0.724 13.529 16796 Z= 0.386 Chirality : 0.043 0.202 1794 Planarity : 0.004 0.040 2131 Dihedral : 18.226 130.720 4747 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.99 % Allowed : 20.73 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1466 helix: 1.01 (0.20), residues: 686 sheet: -0.31 (0.37), residues: 179 loop : 0.48 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.029 0.001 TYR E 67 PHE 0.019 0.002 PHE E 90 TRP 0.078 0.006 TRP E 25 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (12428) covalent geometry : angle 0.71513 / 0.38 (16790) SS BOND : bond 0.36358 / 13.47 ( 3) SS BOND : angle 6.08767 / 3.51 ( 6) hydrogen bonds : bond 0.15669 / 10.59 ( 554) hydrogen bonds : angle 6.85610 / 4.77 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 412 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7823 (tttt) cc_final: 0.7614 (ttmm) REVERT: A 14 ASN cc_start: 0.7844 (m110) cc_final: 0.7604 (m110) REVERT: A 23 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7110 (mtmm) REVERT: A 31 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6348 (mt-10) REVERT: A 47 PHE cc_start: 0.7461 (t80) cc_final: 0.7118 (t80) REVERT: A 52 LYS cc_start: 0.7812 (tptm) cc_final: 0.7435 (ttpt) REVERT: A 56 ASP cc_start: 0.7378 (m-30) cc_final: 0.7101 (m-30) REVERT: A 79 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 119 GLU cc_start: 0.7115 (mp0) cc_final: 0.6866 (mp0) REVERT: A 152 SER cc_start: 0.8289 (p) cc_final: 0.8058 (t) REVERT: A 187 ASP cc_start: 0.7934 (t70) cc_final: 0.7618 (t0) REVERT: A 209 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7972 (ttmm) REVERT: A 211 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 218 ASN cc_start: 0.8133 (t0) cc_final: 0.7753 (t160) REVERT: A 286 ASP cc_start: 0.7020 (m-30) cc_final: 0.6785 (m-30) REVERT: A 316 GLU cc_start: 0.7344 (mp0) cc_final: 0.6988 (mp0) REVERT: A 322 MET cc_start: 0.8105 (mmt) cc_final: 0.7665 (mtp) REVERT: A 341 LYS cc_start: 0.8183 (tptt) cc_final: 0.7834 (mmmm) REVERT: A 384 GLU cc_start: 0.7683 (pp20) cc_final: 0.7453 (pp20) REVERT: A 394 TYR cc_start: 0.7957 (m-80) cc_final: 0.7698 (m-80) REVERT: A 458 MET cc_start: 0.8304 (mmm) cc_final: 0.8099 (mmm) REVERT: A 480 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7693 (mp0) REVERT: A 515 ASP cc_start: 0.7883 (m-30) cc_final: 0.7672 (m-30) REVERT: A 548 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 556 GLU cc_start: 0.6773 (pp20) cc_final: 0.5906 (pp20) REVERT: A 560 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8118 (mppt) REVERT: A 590 SER cc_start: 0.8475 (p) cc_final: 0.8159 (p) REVERT: A 599 GLU cc_start: 0.7260 (pt0) cc_final: 0.7016 (pt0) REVERT: A 612 TYR cc_start: 0.7644 (m-80) cc_final: 0.6655 (m-80) REVERT: A 632 MET cc_start: 0.8376 (mtt) cc_final: 0.8018 (mtt) REVERT: A 634 MET cc_start: 0.8185 (mmp) cc_final: 0.7961 (mmm) REVERT: A 679 ILE cc_start: 0.8982 (mm) cc_final: 0.8758 (mm) REVERT: B 18 ILE cc_start: 0.8166 (mm) cc_final: 0.7926 (OUTLIER) REVERT: B 52 LYS cc_start: 0.8242 (tptm) cc_final: 0.7997 (tppp) REVERT: B 117 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7929 (mtp180) REVERT: B 128 PHE cc_start: 0.7967 (t80) cc_final: 0.7759 (t80) REVERT: B 131 ASN cc_start: 0.8223 (t0) cc_final: 0.8002 (t0) REVERT: B 133 ASP cc_start: 0.7809 (t0) cc_final: 0.7597 (t0) REVERT: B 178 SER cc_start: 0.8089 (p) cc_final: 0.7879 (t) REVERT: B 184 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7808 (tpt-90) REVERT: B 217 GLU cc_start: 0.7032 (mp0) cc_final: 0.6748 (mp0) REVERT: B 227 MET cc_start: 0.8239 (mtp) cc_final: 0.7942 (mtm) REVERT: B 295 ASP cc_start: 0.7838 (t0) cc_final: 0.7470 (t0) REVERT: B 315 ASP cc_start: 0.7434 (p0) cc_final: 0.7119 (p0) REVERT: B 420 MET cc_start: 0.8484 (mmm) cc_final: 0.8073 (mmm) REVERT: B 436 LEU cc_start: 0.8676 (mt) cc_final: 0.8446 (mp) REVERT: B 494 MET cc_start: 0.8526 (mtp) cc_final: 0.8323 (mtp) REVERT: B 550 MET cc_start: 0.8411 (mtm) cc_final: 0.8098 (mtp) REVERT: B 559 LYS cc_start: 0.7980 (mttp) cc_final: 0.7718 (mttm) REVERT: B 581 THR cc_start: 0.8034 (p) cc_final: 0.7162 (t) REVERT: B 598 MET cc_start: 0.7430 (mtp) cc_final: 0.7119 (mtm) REVERT: B 612 TYR cc_start: 0.7908 (m-80) cc_final: 0.7613 (m-80) REVERT: B 631 ASP cc_start: 0.7589 (m-30) cc_final: 0.7336 (m-30) REVERT: B 639 ASP cc_start: 0.7406 (m-30) cc_final: 0.7194 (m-30) REVERT: B 660 ASP cc_start: 0.7020 (m-30) cc_final: 0.6815 (m-30) outliers start: 13 outliers final: 7 residues processed: 418 average time/residue: 0.5704 time to fit residues: 256.2760 Evaluate side-chains 352 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 346 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 296 LYS Chi-restraints excluded: chain B residue 409 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 329 ASN A 410 ASN A 676 HIS B 34 HIS B 180 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 422 HIS B 645 GLN B 676 HIS E 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109569 restraints weight = 17180.783| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.74 r_work: 0.3315 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12431 Z= 0.235 Angle : 0.598 7.663 16796 Z= 0.313 Chirality : 0.046 0.180 1794 Planarity : 0.004 0.060 2131 Dihedral : 10.222 130.426 1795 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 21.42 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1466 helix: 0.91 (0.19), residues: 693 sheet: -0.14 (0.39), residues: 161 loop : 0.16 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 677 TYR 0.016 0.002 TYR A 140 PHE 0.020 0.002 PHE A 492 TRP 0.011 0.002 TRP E 25 HIS 0.011 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (12428) covalent geometry : angle 0.59669 / 0.31 (16790) SS BOND : bond 0.00233 / 0.10 ( 3) SS BOND : angle 2.36523 / 1.28 ( 6) hydrogen bonds : bond 0.04045 / 2.63 ( 554) hydrogen bonds : angle 5.31060 / 3.68 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8116 (tttt) cc_final: 0.7781 (ttmm) REVERT: A 23 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7477 (mppt) REVERT: A 31 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 47 PHE cc_start: 0.7965 (t80) cc_final: 0.7617 (t80) REVERT: A 52 LYS cc_start: 0.7949 (tptm) cc_final: 0.7347 (tppp) REVERT: A 56 ASP cc_start: 0.7749 (m-30) cc_final: 0.7376 (m-30) REVERT: A 119 GLU cc_start: 0.7561 (mp0) cc_final: 0.7229 (mp0) REVERT: A 121 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7699 (tpp-160) REVERT: A 174 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 187 ASP cc_start: 0.8172 (t70) cc_final: 0.7866 (t0) REVERT: A 209 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7846 (ttmm) REVERT: A 211 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7250 (mt-10) REVERT: A 286 ASP cc_start: 0.7597 (m-30) cc_final: 0.7203 (m-30) REVERT: A 312 GLN cc_start: 0.8102 (mt0) cc_final: 0.7810 (mt0) REVERT: A 316 GLU cc_start: 0.7817 (mp0) cc_final: 0.7546 (mp0) REVERT: A 341 LYS cc_start: 0.8434 (mptt) cc_final: 0.8150 (mptt) REVERT: A 384 GLU cc_start: 0.7807 (pp20) cc_final: 0.7174 (pp20) REVERT: A 458 MET cc_start: 0.8339 (mmm) cc_final: 0.7979 (mmm) REVERT: A 480 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 515 ASP cc_start: 0.8135 (m-30) cc_final: 0.7919 (m-30) REVERT: A 541 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6922 (tm-30) REVERT: A 548 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 598 MET cc_start: 0.7935 (mtp) cc_final: 0.7686 (mtp) REVERT: A 599 GLU cc_start: 0.7938 (pt0) cc_final: 0.7733 (pt0) REVERT: A 612 TYR cc_start: 0.7894 (m-80) cc_final: 0.7671 (m-80) REVERT: B 18 ILE cc_start: 0.8437 (mm) cc_final: 0.8216 (mt) REVERT: B 44 ASN cc_start: 0.8237 (m-40) cc_final: 0.7793 (m-40) REVERT: B 52 LYS cc_start: 0.8394 (tptm) cc_final: 0.8155 (tptp) REVERT: B 65 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 117 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7966 (mtp180) REVERT: B 120 ASP cc_start: 0.8285 (m-30) cc_final: 0.8058 (m-30) REVERT: B 133 ASP cc_start: 0.8061 (t0) cc_final: 0.7760 (t0) REVERT: B 217 GLU cc_start: 0.7757 (mp0) cc_final: 0.7331 (mp0) REVERT: B 227 MET cc_start: 0.8413 (mtp) cc_final: 0.8172 (mtp) REVERT: B 240 MET cc_start: 0.1266 (ppp) cc_final: 0.1063 (ppp) REVERT: B 243 ARG cc_start: 0.2516 (OUTLIER) cc_final: 0.1830 (ptm-80) REVERT: B 295 ASP cc_start: 0.8189 (t0) cc_final: 0.7830 (t0) REVERT: B 318 ASP cc_start: 0.7967 (t0) cc_final: 0.7612 (t0) REVERT: B 319 MET cc_start: 0.8475 (tpp) cc_final: 0.8167 (tpt) REVERT: B 420 MET cc_start: 0.8696 (mmm) cc_final: 0.8106 (mmm) REVERT: B 494 MET cc_start: 0.8402 (mtp) cc_final: 0.8061 (mtp) REVERT: B 518 GLU cc_start: 0.7714 (mp0) cc_final: 0.7494 (mm-30) REVERT: B 526 GLU cc_start: 0.7787 (tp30) cc_final: 0.7585 (tp30) REVERT: B 550 MET cc_start: 0.8636 (mtm) cc_final: 0.8351 (mtp) REVERT: B 552 ILE cc_start: 0.8829 (mt) cc_final: 0.8591 (mm) REVERT: B 556 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 581 THR cc_start: 0.8206 (p) cc_final: 0.7697 (t) REVERT: B 598 MET cc_start: 0.8052 (mtp) cc_final: 0.7186 (mtm) REVERT: B 621 ASN cc_start: 0.8225 (p0) cc_final: 0.7966 (p0) REVERT: B 631 ASP cc_start: 0.8154 (m-30) cc_final: 0.7799 (m-30) REVERT: B 660 ASP cc_start: 0.7756 (m-30) cc_final: 0.7501 (m-30) REVERT: B 686 ARG cc_start: 0.7473 (mtp85) cc_final: 0.6820 (mtp85) outliers start: 50 outliers final: 20 residues processed: 382 average time/residue: 0.5778 time to fit residues: 237.7080 Evaluate side-chains 356 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 338 ASN A 410 ASN A 676 HIS B 11 GLN B 14 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 676 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109506 restraints weight = 17258.120| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.76 r_work: 0.3311 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12431 Z= 0.223 Angle : 0.563 7.399 16796 Z= 0.295 Chirality : 0.045 0.179 1794 Planarity : 0.004 0.051 2131 Dihedral : 9.825 130.339 1790 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.21 % Allowed : 22.49 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1466 helix: 0.82 (0.19), residues: 700 sheet: -0.22 (0.39), residues: 161 loop : 0.08 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 350 TYR 0.020 0.002 TYR A 140 PHE 0.018 0.002 PHE B 492 TRP 0.008 0.002 TRP A 9 HIS 0.010 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (12428) covalent geometry : angle 0.56194 / 0.29 (16790) SS BOND : bond 0.00145 / 0.06 ( 3) SS BOND : angle 2.14571 / 1.16 ( 6) hydrogen bonds : bond 0.03744 / 2.44 ( 554) hydrogen bonds : angle 5.17842 / 3.57 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 344 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8112 (tttt) cc_final: 0.7779 (ttmm) REVERT: A 13 ASN cc_start: 0.8687 (t0) cc_final: 0.8477 (t0) REVERT: A 23 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7592 (mtmm) REVERT: A 31 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 47 PHE cc_start: 0.8022 (t80) cc_final: 0.7668 (t80) REVERT: A 52 LYS cc_start: 0.7930 (tptm) cc_final: 0.7244 (tppp) REVERT: A 56 ASP cc_start: 0.7735 (m-30) cc_final: 0.7292 (m-30) REVERT: A 66 GLU cc_start: 0.7389 (tp30) cc_final: 0.7151 (tp30) REVERT: A 119 GLU cc_start: 0.7521 (mp0) cc_final: 0.7236 (mp0) REVERT: A 133 ASP cc_start: 0.7902 (t70) cc_final: 0.7689 (t0) REVERT: A 144 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: A 162 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7892 (ttmt) REVERT: A 187 ASP cc_start: 0.8059 (t70) cc_final: 0.7789 (t0) REVERT: A 209 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7850 (ttmm) REVERT: A 211 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7294 (mt-10) REVERT: A 286 ASP cc_start: 0.7577 (m-30) cc_final: 0.7210 (m-30) REVERT: A 309 GLU cc_start: 0.7721 (tp30) cc_final: 0.7229 (tm-30) REVERT: A 312 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: A 316 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: A 319 MET cc_start: 0.8528 (tpp) cc_final: 0.8241 (tpt) REVERT: A 321 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 322 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7923 (mmm) REVERT: A 331 ARG cc_start: 0.8111 (mpp80) cc_final: 0.7609 (mtp180) REVERT: A 341 LYS cc_start: 0.8431 (mptt) cc_final: 0.8084 (mptt) REVERT: A 362 ASP cc_start: 0.7947 (m-30) cc_final: 0.7202 (m-30) REVERT: A 384 GLU cc_start: 0.7710 (pp20) cc_final: 0.7200 (pp20) REVERT: A 406 ASP cc_start: 0.7520 (m-30) cc_final: 0.7246 (t0) REVERT: A 458 MET cc_start: 0.8246 (mmm) cc_final: 0.8007 (mmm) REVERT: A 480 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 530 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8010 (ptpp) REVERT: A 545 ASN cc_start: 0.8296 (m-40) cc_final: 0.8063 (m110) REVERT: A 548 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 595 MET cc_start: 0.8410 (mmm) cc_final: 0.8104 (mmm) REVERT: A 632 MET cc_start: 0.8570 (mtt) cc_final: 0.8357 (mtt) REVERT: B 18 ILE cc_start: 0.8420 (mm) cc_final: 0.8207 (mt) REVERT: B 46 VAL cc_start: 0.8792 (p) cc_final: 0.8551 (m) REVERT: B 47 PHE cc_start: 0.8212 (t80) cc_final: 0.7871 (t80) REVERT: B 48 PHE cc_start: 0.8460 (m-80) cc_final: 0.8201 (m-80) REVERT: B 52 LYS cc_start: 0.8391 (tptm) cc_final: 0.8141 (tptp) REVERT: B 65 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 120 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: B 133 ASP cc_start: 0.8067 (t0) cc_final: 0.7761 (t0) REVERT: B 184 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7841 (tpt90) REVERT: B 217 GLU cc_start: 0.7790 (mp0) cc_final: 0.7364 (mp0) REVERT: B 227 MET cc_start: 0.8453 (mtp) cc_final: 0.8182 (mtp) REVERT: B 240 MET cc_start: 0.1287 (ppp) cc_final: 0.0859 (ppp) REVERT: B 295 ASP cc_start: 0.8223 (t0) cc_final: 0.7884 (t0) REVERT: B 316 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6907 (tm-30) REVERT: B 318 ASP cc_start: 0.7975 (t0) cc_final: 0.7609 (t0) REVERT: B 319 MET cc_start: 0.8491 (tpp) cc_final: 0.8129 (tpt) REVERT: B 358 ILE cc_start: 0.8679 (mm) cc_final: 0.8474 (mt) REVERT: B 406 ASP cc_start: 0.7331 (m-30) cc_final: 0.7000 (t0) REVERT: B 420 MET cc_start: 0.8711 (mmm) cc_final: 0.8077 (mmm) REVERT: B 494 MET cc_start: 0.8397 (mtp) cc_final: 0.8146 (mtp) REVERT: B 518 GLU cc_start: 0.7755 (mp0) cc_final: 0.7525 (mm-30) REVERT: B 550 MET cc_start: 0.8695 (mtm) cc_final: 0.8419 (mtp) REVERT: B 556 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 570 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8754 (mtp) REVERT: B 598 MET cc_start: 0.7922 (mtp) cc_final: 0.7128 (mtm) REVERT: B 604 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7394 (mmt-90) REVERT: B 621 ASN cc_start: 0.8272 (p0) cc_final: 0.8036 (p0) REVERT: B 660 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7574 (t0) REVERT: B 686 ARG cc_start: 0.7482 (mtp85) cc_final: 0.6812 (mtp85) outliers start: 55 outliers final: 20 residues processed: 367 average time/residue: 0.5496 time to fit residues: 217.4849 Evaluate side-chains 357 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 48 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN B 11 GLN B 14 ASN B 218 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112085 restraints weight = 17340.432| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.77 r_work: 0.3346 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12431 Z= 0.123 Angle : 0.510 5.697 16796 Z= 0.268 Chirality : 0.041 0.171 1794 Planarity : 0.003 0.043 2131 Dihedral : 9.349 132.286 1788 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.14 % Allowed : 23.79 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1466 helix: 1.09 (0.19), residues: 702 sheet: -0.17 (0.41), residues: 161 loop : 0.02 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 677 TYR 0.019 0.001 TYR A 140 PHE 0.015 0.001 PHE A 492 TRP 0.007 0.001 TRP A 9 HIS 0.008 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12428) covalent geometry : angle 0.50811 / 0.27 (16790) SS BOND : bond 0.00158 / 0.08 ( 3) SS BOND : angle 2.23575 / 1.20 ( 6) hydrogen bonds : bond 0.03178 / 2.07 ( 554) hydrogen bonds : angle 4.93552 / 3.41 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8141 (tttt) cc_final: 0.7783 (ttmm) REVERT: A 23 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7578 (mppt) REVERT: A 31 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 47 PHE cc_start: 0.8014 (t80) cc_final: 0.7688 (t80) REVERT: A 52 LYS cc_start: 0.7887 (tptm) cc_final: 0.7194 (tppp) REVERT: A 56 ASP cc_start: 0.7671 (m-30) cc_final: 0.7261 (m-30) REVERT: A 66 GLU cc_start: 0.7391 (tp30) cc_final: 0.7162 (tp30) REVERT: A 119 GLU cc_start: 0.7488 (mp0) cc_final: 0.7229 (mp0) REVERT: A 121 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7573 (tpp-160) REVERT: A 133 ASP cc_start: 0.7778 (t70) cc_final: 0.7577 (t0) REVERT: A 144 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (mtp) REVERT: A 148 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 162 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (ttmt) REVERT: A 174 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 187 ASP cc_start: 0.8090 (t70) cc_final: 0.7806 (t0) REVERT: A 209 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7822 (ttmm) REVERT: A 211 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7239 (mt-10) REVERT: A 235 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7792 (mtm-85) REVERT: A 286 ASP cc_start: 0.7579 (m-30) cc_final: 0.6878 (m-30) REVERT: A 309 GLU cc_start: 0.7735 (tp30) cc_final: 0.7400 (tm-30) REVERT: A 312 GLN cc_start: 0.8104 (mt0) cc_final: 0.7822 (mt0) REVERT: A 316 GLU cc_start: 0.7725 (mp0) cc_final: 0.7449 (mp0) REVERT: A 321 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A 322 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7906 (mmm) REVERT: A 341 LYS cc_start: 0.8425 (mptt) cc_final: 0.8076 (mptt) REVERT: A 362 ASP cc_start: 0.7880 (m-30) cc_final: 0.6956 (m-30) REVERT: A 384 GLU cc_start: 0.7611 (pp20) cc_final: 0.7078 (pp20) REVERT: A 406 ASP cc_start: 0.7381 (m-30) cc_final: 0.7095 (t0) REVERT: A 458 MET cc_start: 0.8250 (mmm) cc_final: 0.8000 (mmm) REVERT: A 466 MET cc_start: 0.8205 (ptt) cc_final: 0.7915 (ptp) REVERT: A 480 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 530 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8029 (ptpp) REVERT: A 545 ASN cc_start: 0.8299 (m-40) cc_final: 0.8029 (m110) REVERT: A 548 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 605 THR cc_start: 0.8160 (m) cc_final: 0.7939 (p) REVERT: A 667 LEU cc_start: 0.8131 (tp) cc_final: 0.7675 (mt) REVERT: A 671 ASP cc_start: 0.7489 (m-30) cc_final: 0.7183 (m-30) REVERT: B 18 ILE cc_start: 0.8393 (mm) cc_final: 0.8179 (mt) REVERT: B 46 VAL cc_start: 0.8773 (p) cc_final: 0.8557 (m) REVERT: B 47 PHE cc_start: 0.8182 (t80) cc_final: 0.7832 (t80) REVERT: B 48 PHE cc_start: 0.8396 (m-80) cc_final: 0.8188 (m-80) REVERT: B 65 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 120 ASP cc_start: 0.8185 (m-30) cc_final: 0.7941 (m-30) REVERT: B 209 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7712 (ttpp) REVERT: B 217 GLU cc_start: 0.7678 (mp0) cc_final: 0.7262 (mp0) REVERT: B 227 MET cc_start: 0.8423 (mtp) cc_final: 0.8104 (mtp) REVERT: B 240 MET cc_start: 0.1273 (ppp) cc_final: 0.0851 (ppp) REVERT: B 295 ASP cc_start: 0.8150 (t0) cc_final: 0.7884 (t0) REVERT: B 312 GLN cc_start: 0.8305 (mt0) cc_final: 0.8098 (pt0) REVERT: B 318 ASP cc_start: 0.7866 (t0) cc_final: 0.7516 (t0) REVERT: B 319 MET cc_start: 0.8497 (tpp) cc_final: 0.8176 (tpt) REVERT: B 406 ASP cc_start: 0.7342 (m-30) cc_final: 0.6955 (t0) REVERT: B 420 MET cc_start: 0.8697 (mmm) cc_final: 0.8093 (mmm) REVERT: B 444 ASP cc_start: 0.7821 (t70) cc_final: 0.7398 (t0) REVERT: B 456 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8122 (mmtm) REVERT: B 494 MET cc_start: 0.8348 (mtp) cc_final: 0.7968 (mtp) REVERT: B 518 GLU cc_start: 0.7762 (mp0) cc_final: 0.7535 (mm-30) REVERT: B 550 MET cc_start: 0.8629 (mtm) cc_final: 0.8339 (mtp) REVERT: B 556 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 586 TYR cc_start: 0.8406 (m-80) cc_final: 0.7642 (m-80) REVERT: B 598 MET cc_start: 0.7724 (mtp) cc_final: 0.7126 (mtm) REVERT: B 621 ASN cc_start: 0.8199 (p0) cc_final: 0.7947 (p0) REVERT: B 631 ASP cc_start: 0.8143 (m-30) cc_final: 0.7750 (m-30) REVERT: B 660 ASP cc_start: 0.7759 (m-30) cc_final: 0.7530 (m-30) REVERT: B 681 THR cc_start: 0.8685 (m) cc_final: 0.8385 (p) REVERT: B 686 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6799 (mtp85) outliers start: 41 outliers final: 16 residues processed: 364 average time/residue: 0.5470 time to fit residues: 214.9451 Evaluate side-chains 343 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 361 GLN B 415 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109795 restraints weight = 17387.240| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.75 r_work: 0.3305 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12431 Z= 0.239 Angle : 0.572 6.203 16796 Z= 0.299 Chirality : 0.045 0.171 1794 Planarity : 0.004 0.043 2131 Dihedral : 9.370 133.604 1779 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.06 % Allowed : 22.88 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1466 helix: 0.88 (0.19), residues: 702 sheet: -0.31 (0.41), residues: 161 loop : -0.03 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 350 TYR 0.019 0.002 TYR A 140 PHE 0.018 0.002 PHE A 261 TRP 0.008 0.002 TRP A 623 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (12428) covalent geometry : angle 0.57077 / 0.30 (16790) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 2.22623 / 1.22 ( 6) hydrogen bonds : bond 0.03675 / 2.41 ( 554) hydrogen bonds : angle 5.09731 / 3.51 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8166 (tttt) cc_final: 0.7812 (ttmm) REVERT: A 11 GLN cc_start: 0.7584 (tt0) cc_final: 0.7148 (tm-30) REVERT: A 23 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7570 (mppt) REVERT: A 47 PHE cc_start: 0.7992 (t80) cc_final: 0.7653 (t80) REVERT: A 52 LYS cc_start: 0.7914 (tptm) cc_final: 0.7254 (tppp) REVERT: A 56 ASP cc_start: 0.7684 (m-30) cc_final: 0.7258 (m-30) REVERT: A 79 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7273 (mt-10) REVERT: A 116 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: A 119 GLU cc_start: 0.7539 (mp0) cc_final: 0.7241 (mp0) REVERT: A 187 ASP cc_start: 0.8033 (t70) cc_final: 0.7763 (t0) REVERT: A 209 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7835 (ttmm) REVERT: A 211 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7256 (mt-10) REVERT: A 217 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 286 ASP cc_start: 0.7570 (m-30) cc_final: 0.6800 (m-30) REVERT: A 294 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7372 (mp0) REVERT: A 312 GLN cc_start: 0.8169 (mt0) cc_final: 0.7853 (mt0) REVERT: A 316 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 319 MET cc_start: 0.8576 (tpp) cc_final: 0.8344 (tpt) REVERT: A 321 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 322 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7874 (mtp) REVERT: A 341 LYS cc_start: 0.8462 (mptt) cc_final: 0.8048 (mptt) REVERT: A 344 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7534 (mp0) REVERT: A 362 ASP cc_start: 0.7897 (m-30) cc_final: 0.6865 (m-30) REVERT: A 406 ASP cc_start: 0.7355 (m-30) cc_final: 0.7080 (t0) REVERT: A 458 MET cc_start: 0.8276 (mmm) cc_final: 0.8028 (mmm) REVERT: A 466 MET cc_start: 0.8291 (ptt) cc_final: 0.8054 (ptp) REVERT: A 530 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (ptpp) REVERT: A 531 TYR cc_start: 0.8371 (m-80) cc_final: 0.7895 (m-80) REVERT: A 545 ASN cc_start: 0.8258 (m-40) cc_final: 0.8054 (m110) REVERT: A 548 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 599 GLU cc_start: 0.7908 (pt0) cc_final: 0.7703 (pm20) REVERT: A 603 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6501 (mm-30) REVERT: A 626 TYR cc_start: 0.8414 (m-80) cc_final: 0.8202 (m-80) REVERT: B 46 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (m) REVERT: B 47 PHE cc_start: 0.8197 (t80) cc_final: 0.7857 (t80) REVERT: B 52 LYS cc_start: 0.8440 (tptm) cc_final: 0.8237 (tptp) REVERT: B 65 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 82 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8080 (mtpt) REVERT: B 184 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7835 (tpt90) REVERT: B 187 ASP cc_start: 0.7790 (t70) cc_final: 0.7535 (t70) REVERT: B 209 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7765 (ttpp) REVERT: B 217 GLU cc_start: 0.7809 (mp0) cc_final: 0.7472 (mp0) REVERT: B 218 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7837 (t0) REVERT: B 240 MET cc_start: 0.1494 (ppp) cc_final: 0.1119 (ppp) REVERT: B 295 ASP cc_start: 0.8232 (t0) cc_final: 0.7905 (t0) REVERT: B 312 GLN cc_start: 0.8405 (mt0) cc_final: 0.8025 (pt0) REVERT: B 318 ASP cc_start: 0.7980 (t0) cc_final: 0.7605 (t0) REVERT: B 319 MET cc_start: 0.8450 (tpp) cc_final: 0.8111 (tpt) REVERT: B 414 LEU cc_start: 0.8067 (mt) cc_final: 0.7801 (mp) REVERT: B 420 MET cc_start: 0.8678 (mmm) cc_final: 0.8052 (mmm) REVERT: B 444 ASP cc_start: 0.7783 (t70) cc_final: 0.7580 (t0) REVERT: B 456 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8101 (mmtm) REVERT: B 494 MET cc_start: 0.8381 (mtp) cc_final: 0.8161 (mtp) REVERT: B 518 GLU cc_start: 0.7738 (mp0) cc_final: 0.7496 (mm-30) REVERT: B 550 MET cc_start: 0.8632 (mtm) cc_final: 0.8369 (mtp) REVERT: B 556 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B 560 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7994 (mtmm) REVERT: B 598 MET cc_start: 0.7791 (mtp) cc_final: 0.7203 (mtm) REVERT: B 620 SER cc_start: 0.8489 (m) cc_final: 0.8233 (p) REVERT: B 631 ASP cc_start: 0.8222 (m-30) cc_final: 0.7855 (m-30) REVERT: B 681 THR cc_start: 0.8776 (m) cc_final: 0.8467 (p) REVERT: B 686 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6823 (mtp85) outliers start: 53 outliers final: 24 residues processed: 354 average time/residue: 0.5450 time to fit residues: 208.0130 Evaluate side-chains 353 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN B 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110451 restraints weight = 17231.536| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.73 r_work: 0.3325 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12431 Z= 0.173 Angle : 0.544 7.317 16796 Z= 0.286 Chirality : 0.043 0.214 1794 Planarity : 0.004 0.041 2131 Dihedral : 9.042 134.168 1779 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.91 % Allowed : 23.18 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1466 helix: 0.97 (0.19), residues: 702 sheet: -0.36 (0.42), residues: 161 loop : -0.06 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 235 TYR 0.022 0.001 TYR A 140 PHE 0.017 0.002 PHE A 492 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (12428) covalent geometry : angle 0.54240 / 0.29 (16790) SS BOND : bond 0.00271 / 0.14 ( 3) SS BOND : angle 2.44167 / 1.32 ( 6) hydrogen bonds : bond 0.03399 / 2.22 ( 554) hydrogen bonds : angle 5.02423 / 3.46 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8115 (tttt) cc_final: 0.7761 (ttmm) REVERT: A 11 GLN cc_start: 0.7602 (tt0) cc_final: 0.7147 (tm-30) REVERT: A 23 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7631 (mppt) REVERT: A 47 PHE cc_start: 0.7993 (t80) cc_final: 0.7667 (t80) REVERT: A 52 LYS cc_start: 0.7885 (tptm) cc_final: 0.7221 (tppp) REVERT: A 56 ASP cc_start: 0.7676 (m-30) cc_final: 0.7253 (m-30) REVERT: A 79 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7235 (mt-10) REVERT: A 102 ASN cc_start: 0.8040 (m110) cc_final: 0.7719 (m-40) REVERT: A 116 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: A 119 GLU cc_start: 0.7518 (mp0) cc_final: 0.7191 (mp0) REVERT: A 144 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: A 161 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7537 (mtp85) REVERT: A 162 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7967 (ttmm) REVERT: A 187 ASP cc_start: 0.8027 (t70) cc_final: 0.7761 (t0) REVERT: A 209 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7853 (ttmm) REVERT: A 211 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7287 (mt-10) REVERT: A 217 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 240 MET cc_start: 0.2174 (tpt) cc_final: 0.1941 (tpt) REVERT: A 286 ASP cc_start: 0.7547 (m-30) cc_final: 0.6786 (m-30) REVERT: A 294 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7370 (mp0) REVERT: A 312 GLN cc_start: 0.8149 (mt0) cc_final: 0.7837 (mt0) REVERT: A 316 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: A 319 MET cc_start: 0.8574 (tpp) cc_final: 0.8301 (tpt) REVERT: A 321 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: A 341 LYS cc_start: 0.8439 (mptt) cc_final: 0.8051 (mptt) REVERT: A 344 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7431 (mp0) REVERT: A 362 ASP cc_start: 0.7838 (m-30) cc_final: 0.6778 (m-30) REVERT: A 406 ASP cc_start: 0.7332 (m-30) cc_final: 0.7045 (t0) REVERT: A 458 MET cc_start: 0.8271 (mmm) cc_final: 0.7970 (mmm) REVERT: A 466 MET cc_start: 0.8246 (ptt) cc_final: 0.7959 (ptp) REVERT: A 530 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8021 (ptpp) REVERT: A 531 TYR cc_start: 0.8342 (m-80) cc_final: 0.7873 (m-80) REVERT: A 545 ASN cc_start: 0.8244 (m-40) cc_final: 0.8026 (m110) REVERT: A 548 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 567 GLU cc_start: 0.7839 (tp30) cc_final: 0.7552 (tp30) REVERT: A 599 GLU cc_start: 0.7862 (pt0) cc_final: 0.7650 (pm20) REVERT: A 626 TYR cc_start: 0.8349 (m-80) cc_final: 0.8140 (m-80) REVERT: B 46 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 47 PHE cc_start: 0.8183 (t80) cc_final: 0.7892 (t80) REVERT: B 65 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 120 ASP cc_start: 0.8206 (m-30) cc_final: 0.7998 (m-30) REVERT: B 184 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7918 (tpt90) REVERT: B 209 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7770 (ttpp) REVERT: B 295 ASP cc_start: 0.8194 (t0) cc_final: 0.7887 (t0) REVERT: B 318 ASP cc_start: 0.7899 (t0) cc_final: 0.7552 (t0) REVERT: B 319 MET cc_start: 0.8484 (tpp) cc_final: 0.8139 (tpt) REVERT: B 406 ASP cc_start: 0.7326 (m-30) cc_final: 0.7048 (t0) REVERT: B 420 MET cc_start: 0.8683 (mmm) cc_final: 0.8051 (mmm) REVERT: B 444 ASP cc_start: 0.7746 (t70) cc_final: 0.7498 (t0) REVERT: B 456 LYS cc_start: 0.8368 (mttm) cc_final: 0.7993 (mmtm) REVERT: B 494 MET cc_start: 0.8368 (mtp) cc_final: 0.8111 (mtp) REVERT: B 518 GLU cc_start: 0.7734 (mp0) cc_final: 0.7512 (mm-30) REVERT: B 550 MET cc_start: 0.8639 (mtm) cc_final: 0.8371 (mtp) REVERT: B 556 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 560 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7992 (mtmm) REVERT: B 598 MET cc_start: 0.7810 (mtp) cc_final: 0.6867 (mtm) REVERT: B 615 MET cc_start: 0.8698 (mmt) cc_final: 0.8451 (mmt) REVERT: B 620 SER cc_start: 0.8458 (m) cc_final: 0.8218 (p) REVERT: B 628 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 681 THR cc_start: 0.8737 (m) cc_final: 0.8452 (p) REVERT: B 686 ARG cc_start: 0.7461 (mtp85) cc_final: 0.6791 (mtp85) REVERT: E 40 GLU cc_start: 0.8047 (mp0) cc_final: 0.7845 (mp0) outliers start: 38 outliers final: 21 residues processed: 357 average time/residue: 0.5707 time to fit residues: 219.7483 Evaluate side-chains 355 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 327 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN B 14 ASN B 218 ASN B 361 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112200 restraints weight = 17133.855| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.70 r_work: 0.3346 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12431 Z= 0.146 Angle : 0.534 7.991 16796 Z= 0.280 Chirality : 0.042 0.201 1794 Planarity : 0.004 0.041 2131 Dihedral : 8.771 134.987 1779 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.60 % Allowed : 24.18 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1466 helix: 1.05 (0.19), residues: 704 sheet: -0.61 (0.40), residues: 173 loop : -0.00 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 677 TYR 0.018 0.001 TYR B 612 PHE 0.017 0.001 PHE B 657 TRP 0.007 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (12428) covalent geometry : angle 0.53289 / 0.28 (16790) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 2.23150 / 1.21 ( 6) hydrogen bonds : bond 0.03253 / 2.13 ( 554) hydrogen bonds : angle 4.95788 / 3.41 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8129 (tttt) cc_final: 0.7783 (ttmm) REVERT: A 11 GLN cc_start: 0.7575 (tt0) cc_final: 0.7160 (tm-30) REVERT: A 23 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7627 (mppt) REVERT: A 47 PHE cc_start: 0.7970 (t80) cc_final: 0.7657 (t80) REVERT: A 52 LYS cc_start: 0.7880 (tptm) cc_final: 0.7150 (tppp) REVERT: A 56 ASP cc_start: 0.7649 (m-30) cc_final: 0.7192 (m-30) REVERT: A 79 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7220 (mt-10) REVERT: A 102 ASN cc_start: 0.8020 (m110) cc_final: 0.7716 (m-40) REVERT: A 116 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: A 119 GLU cc_start: 0.7486 (mp0) cc_final: 0.7227 (mp0) REVERT: A 162 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7905 (ttmm) REVERT: A 187 ASP cc_start: 0.7996 (t70) cc_final: 0.7734 (t0) REVERT: A 209 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7854 (ttmm) REVERT: A 211 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7257 (mt-10) REVERT: A 217 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 240 MET cc_start: 0.2104 (tpt) cc_final: 0.1783 (tpt) REVERT: A 286 ASP cc_start: 0.7522 (m-30) cc_final: 0.6712 (m-30) REVERT: A 294 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7347 (mp0) REVERT: A 312 GLN cc_start: 0.8125 (mt0) cc_final: 0.7817 (mt0) REVERT: A 316 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 319 MET cc_start: 0.8561 (tpp) cc_final: 0.8280 (tpt) REVERT: A 321 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 331 ARG cc_start: 0.8111 (mpp80) cc_final: 0.7641 (mtp180) REVERT: A 341 LYS cc_start: 0.8448 (mptt) cc_final: 0.8052 (mptt) REVERT: A 344 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7415 (mp0) REVERT: A 362 ASP cc_start: 0.7817 (m-30) cc_final: 0.6683 (m-30) REVERT: A 406 ASP cc_start: 0.7268 (m-30) cc_final: 0.7012 (t0) REVERT: A 458 MET cc_start: 0.8237 (mmm) cc_final: 0.7936 (mmm) REVERT: A 466 MET cc_start: 0.8204 (ptt) cc_final: 0.7862 (ptp) REVERT: A 530 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8043 (ptpp) REVERT: A 531 TYR cc_start: 0.8341 (m-80) cc_final: 0.7912 (m-80) REVERT: A 545 ASN cc_start: 0.8251 (m-40) cc_final: 0.8003 (m110) REVERT: A 548 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7786 (tm-30) REVERT: A 567 GLU cc_start: 0.7870 (tp30) cc_final: 0.7560 (tp30) REVERT: A 599 GLU cc_start: 0.7865 (pt0) cc_final: 0.7662 (pm20) REVERT: A 612 TYR cc_start: 0.7906 (m-80) cc_final: 0.7474 (m-80) REVERT: A 634 MET cc_start: 0.8163 (tpt) cc_final: 0.7942 (tpp) REVERT: A 667 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 671 ASP cc_start: 0.7423 (m-30) cc_final: 0.7120 (m-30) REVERT: B 46 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 47 PHE cc_start: 0.8150 (t80) cc_final: 0.7869 (t80) REVERT: B 48 PHE cc_start: 0.8374 (m-80) cc_final: 0.8163 (m-80) REVERT: B 65 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7281 (mm-30) REVERT: B 120 ASP cc_start: 0.8186 (m-30) cc_final: 0.7975 (m-30) REVERT: B 184 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7913 (tpt90) REVERT: B 217 GLU cc_start: 0.7819 (mp0) cc_final: 0.7446 (mp0) REVERT: B 295 ASP cc_start: 0.8124 (t0) cc_final: 0.7879 (t0) REVERT: B 318 ASP cc_start: 0.7845 (t0) cc_final: 0.7436 (t0) REVERT: B 319 MET cc_start: 0.8459 (tpp) cc_final: 0.8120 (tpt) REVERT: B 406 ASP cc_start: 0.7321 (m-30) cc_final: 0.7007 (t0) REVERT: B 420 MET cc_start: 0.8672 (mmm) cc_final: 0.8050 (mmm) REVERT: B 456 LYS cc_start: 0.8379 (mttm) cc_final: 0.8006 (mmtm) REVERT: B 494 MET cc_start: 0.8332 (mtp) cc_final: 0.7957 (mtp) REVERT: B 550 MET cc_start: 0.8542 (mtm) cc_final: 0.8266 (mtp) REVERT: B 556 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 586 TYR cc_start: 0.8377 (m-80) cc_final: 0.7700 (m-80) REVERT: B 598 MET cc_start: 0.7834 (mtp) cc_final: 0.6862 (mtm) REVERT: B 615 MET cc_start: 0.8681 (mmt) cc_final: 0.8416 (mmt) REVERT: B 620 SER cc_start: 0.8471 (m) cc_final: 0.8234 (p) REVERT: B 628 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 660 ASP cc_start: 0.7691 (t0) cc_final: 0.7462 (t0) REVERT: B 681 THR cc_start: 0.8712 (m) cc_final: 0.8416 (p) REVERT: B 686 ARG cc_start: 0.7412 (mtp85) cc_final: 0.6764 (mtp85) outliers start: 34 outliers final: 19 residues processed: 344 average time/residue: 0.5674 time to fit residues: 210.6649 Evaluate side-chains 347 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 321 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 133 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN B 11 GLN B 218 ASN B 361 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112543 restraints weight = 17079.101| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.72 r_work: 0.3347 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12431 Z= 0.150 Angle : 0.541 8.674 16796 Z= 0.283 Chirality : 0.043 0.226 1794 Planarity : 0.003 0.041 2131 Dihedral : 8.651 135.671 1779 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.91 % Allowed : 24.56 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1466 helix: 1.06 (0.19), residues: 704 sheet: -0.61 (0.40), residues: 173 loop : -0.04 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.019 0.001 TYR A 140 PHE 0.019 0.002 PHE B 657 TRP 0.007 0.001 TRP B 9 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12428) covalent geometry : angle 0.53910 / 0.28 (16790) SS BOND : bond 0.00193 / 0.10 ( 3) SS BOND : angle 2.17681 / 1.18 ( 6) hydrogen bonds : bond 0.03233 / 2.11 ( 554) hydrogen bonds : angle 4.94046 / 3.40 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8120 (tttt) cc_final: 0.7769 (ttmm) REVERT: A 19 GLN cc_start: 0.8275 (mt0) cc_final: 0.7974 (mt0) REVERT: A 20 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7989 (ttmm) REVERT: A 47 PHE cc_start: 0.7945 (t80) cc_final: 0.7629 (t80) REVERT: A 52 LYS cc_start: 0.7898 (tptm) cc_final: 0.7221 (tppp) REVERT: A 56 ASP cc_start: 0.7651 (m-30) cc_final: 0.7229 (m-30) REVERT: A 79 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7229 (mt-10) REVERT: A 102 ASN cc_start: 0.8007 (m110) cc_final: 0.7712 (m-40) REVERT: A 113 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.6903 (mptt) REVERT: A 116 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: A 119 GLU cc_start: 0.7496 (mp0) cc_final: 0.7241 (mp0) REVERT: A 144 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: A 152 SER cc_start: 0.8411 (p) cc_final: 0.8154 (t) REVERT: A 187 ASP cc_start: 0.8013 (t70) cc_final: 0.7732 (t0) REVERT: A 209 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7843 (ttmm) REVERT: A 211 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7262 (mt-10) REVERT: A 217 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 240 MET cc_start: 0.2101 (tpt) cc_final: 0.1829 (tpt) REVERT: A 286 ASP cc_start: 0.7526 (m-30) cc_final: 0.6720 (m-30) REVERT: A 294 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7335 (mp0) REVERT: A 312 GLN cc_start: 0.8085 (mt0) cc_final: 0.7771 (mt0) REVERT: A 316 GLU cc_start: 0.7751 (mp0) cc_final: 0.7364 (mp0) REVERT: A 319 MET cc_start: 0.8578 (tpp) cc_final: 0.8302 (tpt) REVERT: A 321 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 341 LYS cc_start: 0.8436 (mptt) cc_final: 0.8039 (mptt) REVERT: A 344 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7431 (mp0) REVERT: A 362 ASP cc_start: 0.7827 (m-30) cc_final: 0.6710 (m-30) REVERT: A 406 ASP cc_start: 0.7330 (m-30) cc_final: 0.7063 (t0) REVERT: A 458 MET cc_start: 0.8234 (mmm) cc_final: 0.7971 (mmm) REVERT: A 466 MET cc_start: 0.8165 (ptt) cc_final: 0.7861 (ptp) REVERT: A 530 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (ptpp) REVERT: A 531 TYR cc_start: 0.8328 (m-80) cc_final: 0.7857 (m-80) REVERT: A 545 ASN cc_start: 0.8259 (m-40) cc_final: 0.8018 (m110) REVERT: A 548 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 567 GLU cc_start: 0.7884 (tp30) cc_final: 0.7504 (tp30) REVERT: A 667 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 671 ASP cc_start: 0.7435 (m-30) cc_final: 0.7127 (m-30) REVERT: A 686 ARG cc_start: 0.7375 (mtp85) cc_final: 0.6917 (mtp85) REVERT: B 46 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8475 (m) REVERT: B 47 PHE cc_start: 0.8151 (t80) cc_final: 0.7873 (t80) REVERT: B 65 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 87 LYS cc_start: 0.8135 (tptp) cc_final: 0.7882 (tmtm) REVERT: B 120 ASP cc_start: 0.8197 (m-30) cc_final: 0.7986 (m-30) REVERT: B 184 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.7923 (tpt90) REVERT: B 217 GLU cc_start: 0.7892 (mp0) cc_final: 0.7395 (mp0) REVERT: B 295 ASP cc_start: 0.8085 (t0) cc_final: 0.7850 (t0) REVERT: B 318 ASP cc_start: 0.7845 (t0) cc_final: 0.7436 (t0) REVERT: B 319 MET cc_start: 0.8453 (tpp) cc_final: 0.8101 (tpt) REVERT: B 393 SER cc_start: 0.8209 (t) cc_final: 0.7963 (m) REVERT: B 406 ASP cc_start: 0.7319 (m-30) cc_final: 0.6993 (t0) REVERT: B 420 MET cc_start: 0.8672 (mmm) cc_final: 0.8015 (mmm) REVERT: B 456 LYS cc_start: 0.8378 (mttm) cc_final: 0.8009 (mmtm) REVERT: B 494 MET cc_start: 0.8336 (mtp) cc_final: 0.8000 (mtp) REVERT: B 550 MET cc_start: 0.8494 (mtm) cc_final: 0.8264 (mtp) REVERT: B 556 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 586 TYR cc_start: 0.8379 (m-80) cc_final: 0.7699 (m-80) REVERT: B 598 MET cc_start: 0.7868 (mtp) cc_final: 0.6925 (mtm) REVERT: B 603 GLU cc_start: 0.6885 (tp30) cc_final: 0.6675 (mm-30) REVERT: B 604 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7389 (mmt-90) REVERT: B 620 SER cc_start: 0.8502 (m) cc_final: 0.8255 (p) REVERT: B 628 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6750 (mm-30) REVERT: B 660 ASP cc_start: 0.7704 (t0) cc_final: 0.7483 (t0) REVERT: B 681 THR cc_start: 0.8730 (m) cc_final: 0.8383 (p) REVERT: B 686 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6856 (mtp85) outliers start: 38 outliers final: 21 residues processed: 348 average time/residue: 0.5300 time to fit residues: 199.4428 Evaluate side-chains 350 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 322 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 125 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN B 11 GLN B 14 ASN B 218 ASN B 361 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110465 restraints weight = 17160.037| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.68 r_work: 0.3331 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12431 Z= 0.210 Angle : 0.580 8.916 16796 Z= 0.304 Chirality : 0.045 0.240 1794 Planarity : 0.004 0.042 2131 Dihedral : 8.786 136.362 1779 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.75 % Allowed : 25.02 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1466 helix: 0.90 (0.19), residues: 704 sheet: -0.67 (0.40), residues: 173 loop : -0.01 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 677 TYR 0.020 0.002 TYR A 140 PHE 0.023 0.002 PHE A 564 TRP 0.007 0.002 TRP A 623 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (12428) covalent geometry : angle 0.57861 / 0.30 (16790) SS BOND : bond 0.00226 / 0.11 ( 3) SS BOND : angle 2.39973 / 1.31 ( 6) hydrogen bonds : bond 0.03488 / 2.28 ( 554) hydrogen bonds : angle 5.07671 / 3.49 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8141 (tttt) cc_final: 0.7784 (ttmm) REVERT: A 19 GLN cc_start: 0.8324 (mt0) cc_final: 0.8095 (mt0) REVERT: A 23 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7557 (mtmm) REVERT: A 47 PHE cc_start: 0.7934 (t80) cc_final: 0.7599 (t80) REVERT: A 52 LYS cc_start: 0.7912 (tptm) cc_final: 0.7199 (tppp) REVERT: A 56 ASP cc_start: 0.7670 (m-30) cc_final: 0.7216 (m-30) REVERT: A 79 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7240 (mt-10) REVERT: A 102 ASN cc_start: 0.8047 (m110) cc_final: 0.7754 (m-40) REVERT: A 119 GLU cc_start: 0.7494 (mp0) cc_final: 0.7229 (mp0) REVERT: A 144 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: A 152 SER cc_start: 0.8397 (p) cc_final: 0.8122 (t) REVERT: A 187 ASP cc_start: 0.7995 (t70) cc_final: 0.7725 (t0) REVERT: A 209 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7835 (ttmm) REVERT: A 211 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7264 (mt-10) REVERT: A 217 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 240 MET cc_start: 0.2086 (tpt) cc_final: 0.1809 (tpt) REVERT: A 286 ASP cc_start: 0.7514 (m-30) cc_final: 0.6709 (m-30) REVERT: A 294 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7453 (mp0) REVERT: A 312 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: A 316 GLU cc_start: 0.7789 (mp0) cc_final: 0.7371 (mp0) REVERT: A 319 MET cc_start: 0.8573 (tpp) cc_final: 0.8321 (tpt) REVERT: A 321 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 322 MET cc_start: 0.8111 (mtp) cc_final: 0.7888 (mtp) REVERT: A 331 ARG cc_start: 0.8148 (mpp80) cc_final: 0.7694 (mtp180) REVERT: A 341 LYS cc_start: 0.8448 (mptt) cc_final: 0.8050 (mptt) REVERT: A 344 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7511 (mp0) REVERT: A 362 ASP cc_start: 0.7853 (m-30) cc_final: 0.6719 (m-30) REVERT: A 406 ASP cc_start: 0.7379 (m-30) cc_final: 0.7097 (t0) REVERT: A 458 MET cc_start: 0.8235 (mmm) cc_final: 0.7975 (mmm) REVERT: A 466 MET cc_start: 0.8221 (ptt) cc_final: 0.7963 (ptp) REVERT: A 530 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8054 (ptpp) REVERT: A 531 TYR cc_start: 0.8335 (m-80) cc_final: 0.7913 (m-80) REVERT: A 545 ASN cc_start: 0.8238 (m-40) cc_final: 0.8017 (m110) REVERT: A 548 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 567 GLU cc_start: 0.7925 (tp30) cc_final: 0.7508 (tp30) REVERT: A 612 TYR cc_start: 0.7726 (m-80) cc_final: 0.7420 (m-80) REVERT: A 686 ARG cc_start: 0.7346 (mtp85) cc_final: 0.6901 (mtp85) REVERT: B 23 LYS cc_start: 0.7925 (mptm) cc_final: 0.7714 (mmtp) REVERT: B 46 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (m) REVERT: B 47 PHE cc_start: 0.8151 (t80) cc_final: 0.7864 (t80) REVERT: B 48 PHE cc_start: 0.8399 (m-80) cc_final: 0.8176 (m-80) REVERT: B 65 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 82 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8047 (mtpt) REVERT: B 115 LEU cc_start: 0.8826 (mt) cc_final: 0.8596 (mp) REVERT: B 136 LYS cc_start: 0.8234 (mmmm) cc_final: 0.8027 (tptp) REVERT: B 184 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7886 (tpt90) REVERT: B 217 GLU cc_start: 0.7900 (mp0) cc_final: 0.7427 (mp0) REVERT: B 295 ASP cc_start: 0.8150 (t0) cc_final: 0.7931 (t0) REVERT: B 316 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6600 (tm-30) REVERT: B 318 ASP cc_start: 0.7815 (t0) cc_final: 0.7425 (t0) REVERT: B 319 MET cc_start: 0.8422 (tpp) cc_final: 0.8123 (tpt) REVERT: B 406 ASP cc_start: 0.7352 (m-30) cc_final: 0.6992 (t0) REVERT: B 420 MET cc_start: 0.8675 (mmm) cc_final: 0.8052 (mmm) REVERT: B 456 LYS cc_start: 0.8394 (mttm) cc_final: 0.8010 (mmtm) REVERT: B 494 MET cc_start: 0.8335 (mtp) cc_final: 0.8076 (mtp) REVERT: B 550 MET cc_start: 0.8587 (mtm) cc_final: 0.8321 (mtp) REVERT: B 556 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 557 ASP cc_start: 0.8022 (m-30) cc_final: 0.7817 (m-30) REVERT: B 560 LYS cc_start: 0.8225 (mtmm) cc_final: 0.8005 (mtmm) REVERT: B 598 MET cc_start: 0.7848 (mtp) cc_final: 0.6906 (mtm) REVERT: B 599 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7800 (mp0) REVERT: B 628 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 631 ASP cc_start: 0.8110 (m-30) cc_final: 0.7834 (m-30) REVERT: B 655 THR cc_start: 0.8285 (m) cc_final: 0.7969 (p) REVERT: B 660 ASP cc_start: 0.7779 (t0) cc_final: 0.7550 (t0) REVERT: B 681 THR cc_start: 0.8764 (m) cc_final: 0.8465 (p) REVERT: B 686 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6875 (mtp85) outliers start: 36 outliers final: 22 residues processed: 347 average time/residue: 0.5708 time to fit residues: 213.5940 Evaluate side-chains 350 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 118 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 137 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN B 11 GLN B 218 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112810 restraints weight = 17244.159| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.72 r_work: 0.3346 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12431 Z= 0.139 Angle : 0.565 9.159 16796 Z= 0.294 Chirality : 0.043 0.229 1794 Planarity : 0.004 0.040 2131 Dihedral : 8.560 136.554 1779 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 25.33 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1466 helix: 1.04 (0.19), residues: 704 sheet: -0.76 (0.40), residues: 173 loop : -0.07 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 677 TYR 0.019 0.001 TYR A 140 PHE 0.021 0.001 PHE A 564 TRP 0.007 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (12428) covalent geometry : angle 0.56331 / 0.29 (16790) SS BOND : bond 0.00196 / 0.10 ( 3) SS BOND : angle 2.17544 / 1.18 ( 6) hydrogen bonds : bond 0.03218 / 2.10 ( 554) hydrogen bonds : angle 4.96827 / 3.42 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8120 (tttt) cc_final: 0.7758 (ttmm) REVERT: A 19 GLN cc_start: 0.8388 (mt0) cc_final: 0.8141 (mt0) REVERT: A 23 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7491 (mtmm) REVERT: A 25 GLN cc_start: 0.7824 (mt0) cc_final: 0.7234 (mt0) REVERT: A 47 PHE cc_start: 0.7933 (t80) cc_final: 0.7633 (t80) REVERT: A 52 LYS cc_start: 0.7909 (tptm) cc_final: 0.7206 (tppp) REVERT: A 56 ASP cc_start: 0.7584 (m-30) cc_final: 0.7167 (m-30) REVERT: A 79 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7241 (mt-10) REVERT: A 102 ASN cc_start: 0.8005 (m110) cc_final: 0.7721 (m-40) REVERT: A 113 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.6941 (mptt) REVERT: A 119 GLU cc_start: 0.7498 (mp0) cc_final: 0.7254 (mp0) REVERT: A 144 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7989 (mtp) REVERT: A 152 SER cc_start: 0.8437 (p) cc_final: 0.8178 (t) REVERT: A 187 ASP cc_start: 0.8015 (t70) cc_final: 0.7740 (t0) REVERT: A 209 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7854 (ttmm) REVERT: A 211 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7275 (mt-10) REVERT: A 217 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 240 MET cc_start: 0.2044 (tpt) cc_final: 0.1764 (tpt) REVERT: A 286 ASP cc_start: 0.7515 (m-30) cc_final: 0.6678 (m-30) REVERT: A 294 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7430 (mp0) REVERT: A 312 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: A 316 GLU cc_start: 0.7710 (mp0) cc_final: 0.7341 (mp0) REVERT: A 319 MET cc_start: 0.8566 (tpp) cc_final: 0.8290 (tpt) REVERT: A 321 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 331 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7608 (mtp180) REVERT: A 341 LYS cc_start: 0.8452 (mptt) cc_final: 0.8110 (mptt) REVERT: A 344 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7455 (mp0) REVERT: A 362 ASP cc_start: 0.7781 (m-30) cc_final: 0.6639 (m-30) REVERT: A 386 LEU cc_start: 0.8599 (mt) cc_final: 0.8322 (mt) REVERT: A 406 ASP cc_start: 0.7327 (m-30) cc_final: 0.7055 (t0) REVERT: A 458 MET cc_start: 0.8222 (mmm) cc_final: 0.7959 (mmm) REVERT: A 466 MET cc_start: 0.8174 (ptt) cc_final: 0.7871 (ptp) REVERT: A 530 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8032 (ptpp) REVERT: A 531 TYR cc_start: 0.8293 (m-80) cc_final: 0.7829 (m-80) REVERT: A 545 ASN cc_start: 0.8276 (m-40) cc_final: 0.8026 (m110) REVERT: A 548 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 567 GLU cc_start: 0.7927 (tp30) cc_final: 0.7546 (tp30) REVERT: A 612 TYR cc_start: 0.7822 (m-80) cc_final: 0.7359 (m-80) REVERT: A 667 LEU cc_start: 0.8131 (mt) cc_final: 0.7779 (tp) REVERT: A 671 ASP cc_start: 0.7449 (m-30) cc_final: 0.7139 (m-30) REVERT: A 686 ARG cc_start: 0.7317 (mtp85) cc_final: 0.6840 (mtp85) REVERT: B 23 LYS cc_start: 0.7842 (mptm) cc_final: 0.7621 (mmtp) REVERT: B 46 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 47 PHE cc_start: 0.8101 (t80) cc_final: 0.7824 (t80) REVERT: B 65 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 87 LYS cc_start: 0.8123 (tptp) cc_final: 0.7868 (tmtm) REVERT: B 136 LYS cc_start: 0.8238 (mmmm) cc_final: 0.8007 (tppp) REVERT: B 184 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.7944 (tpt90) REVERT: B 209 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7772 (ttpp) REVERT: B 217 GLU cc_start: 0.7925 (mp0) cc_final: 0.7435 (mp0) REVERT: B 295 ASP cc_start: 0.8107 (t0) cc_final: 0.7896 (t0) REVERT: B 316 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 406 ASP cc_start: 0.7312 (m-30) cc_final: 0.6981 (t0) REVERT: B 420 MET cc_start: 0.8654 (mmm) cc_final: 0.7991 (mmm) REVERT: B 456 LYS cc_start: 0.8361 (mttm) cc_final: 0.8001 (mmtm) REVERT: B 494 MET cc_start: 0.8320 (mtp) cc_final: 0.7950 (mtp) REVERT: B 550 MET cc_start: 0.8512 (mtm) cc_final: 0.8261 (mtp) REVERT: B 556 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 560 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7951 (mtmm) REVERT: B 586 TYR cc_start: 0.8367 (m-80) cc_final: 0.7715 (m-80) REVERT: B 598 MET cc_start: 0.7846 (mtp) cc_final: 0.6921 (mtm) REVERT: B 628 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6746 (mm-30) REVERT: B 655 THR cc_start: 0.8290 (m) cc_final: 0.7980 (p) REVERT: B 660 ASP cc_start: 0.7767 (t0) cc_final: 0.7535 (t0) REVERT: B 681 THR cc_start: 0.8718 (m) cc_final: 0.8382 (p) REVERT: B 686 ARG cc_start: 0.7393 (mtp85) cc_final: 0.6806 (mtp85) outliers start: 30 outliers final: 21 residues processed: 341 average time/residue: 0.6016 time to fit residues: 221.2481 Evaluate side-chains 350 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN A 455 ASN B 11 GLN B 218 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112106 restraints weight = 17185.198| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.70 r_work: 0.3358 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12431 Z= 0.140 Angle : 0.571 9.833 16796 Z= 0.296 Chirality : 0.043 0.228 1794 Planarity : 0.004 0.041 2131 Dihedral : 8.478 137.139 1779 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.84 % Allowed : 26.09 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1466 helix: 1.09 (0.20), residues: 700 sheet: -0.79 (0.40), residues: 173 loop : -0.07 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 677 TYR 0.021 0.001 TYR A 140 PHE 0.029 0.001 PHE A 564 TRP 0.007 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (12428) covalent geometry : angle 0.56989 / 0.30 (16790) SS BOND : bond 0.00190 / 0.09 ( 3) SS BOND : angle 2.07830 / 1.13 ( 6) hydrogen bonds : bond 0.03196 / 2.09 ( 554) hydrogen bonds : angle 4.95155 / 3.40 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4637.16 seconds wall clock time: 79 minutes 45.36 seconds (4785.36 seconds total)