Starting phenix.real_space_refine on Fri Jul 3 01:37:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxc_45004/07_2026/9bxc_45004.map" } resolution = 2.76 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= 0.003 sd= 0.101 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 60 5.16 5 C 7284 2.51 5 N 1898 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 11496 Number of models: 1 Model: "" Number of chains: 6 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: "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: 2.72, per 1000 atoms: 0.24 Number of scatterers: 11496 At special positions: 0 Unit cell: (91.26, 84.162, 131.82, 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 60 16.00 P 16 15.00 Mg 2 11.99 O 2236 8.00 N 1898 7.00 C 7284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, 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 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: 1.10 Conformation dependent library (CDL) restraints added in 502.8 milliseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 53.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.259A 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: 3.788A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.231A 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: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.634A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A 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: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A 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: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.256A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (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: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.818A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A 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 659 519 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3683 1.34 - 1.46: 2824 1.46 - 1.58: 5105 1.58 - 1.70: 24 1.70 - 1.82: 112 Bond restraints: 11748 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 4.92e+01 bond pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " ideal model delta sigma weight residual 1.748 1.611 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O3A TTP B 802 " pdb=" PB TTP B 802 " 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 A 801 " pdb=" PB TTP A 801 " 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 6.43e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15650 2.06 - 4.13: 148 4.13 - 6.19: 53 6.19 - 8.25: 11 8.25 - 10.32: 6 Bond angle restraints: 15868 Sorted by residual: angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 113.71 109.94 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.91 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CA PRO D 314 " pdb=" N PRO D 314 " pdb=" CD PRO D 314 " ideal model delta sigma weight residual 112.00 107.19 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" O1A TTP B 802 " pdb=" PA TTP B 802 " pdb=" O2A TTP B 802 " ideal model delta sigma weight residual 121.23 110.97 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA VAL C 312 " pdb=" CB VAL C 312 " pdb=" CG1 VAL C 312 " ideal model delta sigma weight residual 110.40 116.18 -5.78 1.70e+00 3.46e-01 1.16e+01 ... (remaining 15863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 6470 26.14 - 52.28: 587 52.28 - 78.43: 81 78.43 - 104.57: 8 104.57 - 130.71: 2 Dihedral angle restraints: 7148 sinusoidal: 3024 harmonic: 4124 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 -170.25 84.25 1 1.00e+01 1.00e-02 8.64e+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 -103.69 130.71 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 -101.13 128.15 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 7145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1050 0.031 - 0.063: 455 0.063 - 0.094: 114 0.094 - 0.126: 61 0.126 - 0.157: 6 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA ASP A 398 " pdb=" N ASP A 398 " pdb=" C ASP A 398 " pdb=" CB ASP A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ASP A 215 " pdb=" N ASP A 215 " pdb=" C ASP A 215 " pdb=" CB ASP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE B 652 " pdb=" N ILE B 652 " pdb=" C ILE B 652 " pdb=" CB ILE B 652 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1683 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 37 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C PHE B 37 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE B 37 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 38 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 37 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C PHE A 37 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 37 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 313 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO D 314 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 314 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 314 " 0.023 5.00e-02 4.00e+02 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 270 2.67 - 3.23: 11141 3.23 - 3.79: 20492 3.79 - 4.34: 28879 4.34 - 4.90: 46230 Nonbonded interactions: 107012 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 107007 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: 0.03 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.140 11750 Z= 0.177 Angle : 0.623 10.316 15872 Z= 0.306 Chirality : 0.040 0.157 1686 Planarity : 0.003 0.040 2014 Dihedral : 18.563 130.709 4490 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.81 % Allowed : 22.00 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.22), residues: 1382 helix: 1.08 (0.20), residues: 650 sheet: -0.60 (0.39), residues: 154 loop : 0.51 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.008 0.001 TYR A 471 PHE 0.015 0.001 PHE A 100 TRP 0.006 0.001 TRP B 9 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (11748) covalent geometry : angle 0.62110 / 0.30 (15868) SS BOND : bond 0.00403 / 0.21 ( 2) SS BOND : angle 2.90084 / 1.56 ( 4) hydrogen bonds : bond 0.15268 / 10.60 ( 517) hydrogen bonds : angle 6.76712 / 4.63 ( 1497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6766 (mp0) REVERT: A 366 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8328 (mtpt) REVERT: B 11 GLN cc_start: 0.6969 (tt0) cc_final: 0.6520 (tt0) REVERT: B 240 MET cc_start: 0.3881 (ppp) cc_final: 0.3387 (ppp) REVERT: B 393 SER cc_start: 0.8840 (t) cc_final: 0.8568 (t) outliers start: 10 outliers final: 6 residues processed: 172 average time/residue: 0.5671 time to fit residues: 105.5775 Evaluate side-chains 152 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN A 320 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121433 restraints weight = 11392.381| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.41 r_work: 0.3209 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11750 Z= 0.239 Angle : 0.586 6.541 15872 Z= 0.310 Chirality : 0.044 0.169 1686 Planarity : 0.004 0.040 2014 Dihedral : 10.411 129.373 1711 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.81 % Allowed : 19.16 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1382 helix: 0.84 (0.20), residues: 660 sheet: -0.62 (0.43), residues: 134 loop : 0.17 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 331 TYR 0.015 0.002 TYR B 574 PHE 0.019 0.002 PHE A 100 TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (11748) covalent geometry : angle 0.58293 / 0.31 (15868) SS BOND : bond 0.00425 / 0.20 ( 2) SS BOND : angle 3.72336 / 1.88 ( 4) hydrogen bonds : bond 0.04384 / 2.91 ( 517) hydrogen bonds : angle 5.54126 / 3.75 ( 1497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: A 75 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7256 (mp0) REVERT: A 316 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 632 MET cc_start: 0.8996 (mtt) cc_final: 0.8268 (mtt) REVERT: A 658 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 11 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: B 15 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: B 43 GLN cc_start: 0.7733 (mt0) cc_final: 0.7501 (mt0) REVERT: B 240 MET cc_start: 0.3784 (OUTLIER) cc_final: 0.3159 (ppp) REVERT: B 341 LYS cc_start: 0.7845 (mmmm) cc_final: 0.7280 (mtpm) REVERT: B 384 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: B 658 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8095 (mt) outliers start: 47 outliers final: 22 residues processed: 181 average time/residue: 0.5083 time to fit residues: 100.2804 Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113713 restraints weight = 12331.333| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.48 r_work: 0.3090 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11750 Z= 0.129 Angle : 0.513 11.789 15872 Z= 0.270 Chirality : 0.041 0.189 1686 Planarity : 0.003 0.038 2014 Dihedral : 9.565 130.214 1703 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.60 % Allowed : 20.70 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.70 (0.22), residues: 1382 helix: 1.09 (0.20), residues: 660 sheet: -0.55 (0.43), residues: 134 loop : 0.16 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 331 TYR 0.011 0.001 TYR B 574 PHE 0.017 0.001 PHE A 100 TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11748) covalent geometry : angle 0.50642 / 0.27 (15868) SS BOND : bond 0.00093 / 0.04 ( 2) SS BOND : angle 5.18028 / 2.59 ( 4) hydrogen bonds : bond 0.03475 / 2.32 ( 517) hydrogen bonds : angle 5.07831 / 3.42 ( 1497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.392 Fit side-chains REVERT: A 75 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6923 (mp0) REVERT: A 632 MET cc_start: 0.8901 (mtt) cc_final: 0.8185 (mtt) REVERT: A 658 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8183 (mp) REVERT: B 11 GLN cc_start: 0.6421 (tt0) cc_final: 0.6111 (tt0) REVERT: B 15 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: B 43 GLN cc_start: 0.7657 (mt0) cc_final: 0.7397 (mt0) REVERT: B 240 MET cc_start: 0.3623 (ppp) cc_final: 0.3031 (ppp) REVERT: B 348 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7633 (ptp) REVERT: B 384 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: B 393 SER cc_start: 0.8664 (t) cc_final: 0.8381 (t) REVERT: B 658 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7582 (mt) outliers start: 32 outliers final: 10 residues processed: 176 average time/residue: 0.4999 time to fit residues: 96.2780 Evaluate side-chains 157 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN A 329 ASN A 410 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 329 ASN B 474 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119269 restraints weight = 11532.791| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.40 r_work: 0.3169 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11750 Z= 0.298 Angle : 0.619 9.849 15872 Z= 0.324 Chirality : 0.046 0.163 1686 Planarity : 0.004 0.042 2014 Dihedral : 9.601 130.165 1696 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.65 % Allowed : 19.32 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.27 (0.22), residues: 1382 helix: 0.67 (0.20), residues: 660 sheet: -0.71 (0.43), residues: 134 loop : 0.01 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.014 0.002 TYR B 101 PHE 0.022 0.002 PHE A 100 TRP 0.006 0.002 TRP A 9 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (11748) covalent geometry : angle 0.61400 / 0.32 (15868) SS BOND : bond 0.00542 / 0.28 ( 2) SS BOND : angle 4.88063 / 2.53 ( 4) hydrogen bonds : bond 0.04327 / 2.87 ( 517) hydrogen bonds : angle 5.44011 / 3.66 ( 1497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7180 (mp0) REVERT: A 316 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 545 ASN cc_start: 0.8610 (m-40) cc_final: 0.8281 (m-40) REVERT: A 603 GLU cc_start: 0.7299 (tt0) cc_final: 0.6644 (tt0) REVERT: A 632 MET cc_start: 0.9015 (mtt) cc_final: 0.8342 (mtt) REVERT: A 658 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 667 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 11 GLN cc_start: 0.6881 (tt0) cc_final: 0.6500 (tt0) REVERT: B 15 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: B 43 GLN cc_start: 0.7770 (mt0) cc_final: 0.7558 (mt0) REVERT: B 131 ASN cc_start: 0.8121 (t0) cc_final: 0.7867 (t0) REVERT: B 240 MET cc_start: 0.3648 (OUTLIER) cc_final: 0.2953 (ppp) REVERT: B 309 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: B 384 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: B 393 SER cc_start: 0.8904 (t) cc_final: 0.8639 (t) REVERT: B 639 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: B 658 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7943 (mt) outliers start: 45 outliers final: 19 residues processed: 171 average time/residue: 0.5738 time to fit residues: 106.2916 Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 320 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125474 restraints weight = 11472.907| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.38 r_work: 0.3258 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.134 Angle : 0.498 7.490 15872 Z= 0.264 Chirality : 0.041 0.164 1686 Planarity : 0.003 0.039 2014 Dihedral : 9.241 131.141 1696 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 21.10 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.52 (0.22), residues: 1382 helix: 1.00 (0.20), residues: 660 sheet: -0.78 (0.43), residues: 134 loop : 0.02 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 331 TYR 0.011 0.001 TYR A 574 PHE 0.017 0.001 PHE B 100 TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (11748) covalent geometry : angle 0.49578 / 0.26 (15868) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 3.10860 / 1.63 ( 4) hydrogen bonds : bond 0.03378 / 2.25 ( 517) hydrogen bonds : angle 5.04781 / 3.40 ( 1497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7124 (mp0) REVERT: A 95 MET cc_start: 0.8475 (tpp) cc_final: 0.8197 (mmm) REVERT: A 316 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 362 ASP cc_start: 0.8092 (m-30) cc_final: 0.7872 (m-30) REVERT: A 545 ASN cc_start: 0.8590 (m-40) cc_final: 0.8274 (m-40) REVERT: A 611 THR cc_start: 0.7587 (t) cc_final: 0.7351 (t) REVERT: A 632 MET cc_start: 0.9034 (mtt) cc_final: 0.8356 (mtt) REVERT: A 658 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 11 GLN cc_start: 0.6769 (tt0) cc_final: 0.6485 (tt0) REVERT: B 16 ILE cc_start: 0.7990 (mm) cc_final: 0.7789 (mm) REVERT: B 43 GLN cc_start: 0.7766 (mt0) cc_final: 0.7503 (mt0) REVERT: B 184 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8451 (ttm-80) REVERT: B 240 MET cc_start: 0.3687 (OUTLIER) cc_final: 0.3172 (ppp) REVERT: B 341 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7308 (mtpt) REVERT: B 348 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7855 (ptp) REVERT: B 384 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7959 (pp20) REVERT: B 393 SER cc_start: 0.8826 (t) cc_final: 0.8566 (t) REVERT: B 421 GLU cc_start: 0.8137 (pt0) cc_final: 0.7798 (pp20) REVERT: B 658 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7898 (mt) outliers start: 33 outliers final: 14 residues processed: 177 average time/residue: 0.5663 time to fit residues: 108.9021 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN A 304 HIS ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118721 restraints weight = 11520.245| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.39 r_work: 0.3133 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11750 Z= 0.314 Angle : 0.624 8.123 15872 Z= 0.327 Chirality : 0.046 0.157 1686 Planarity : 0.004 0.043 2014 Dihedral : 9.561 130.532 1696 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.41 % Allowed : 20.54 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.15 (0.22), residues: 1382 helix: 0.61 (0.20), residues: 660 sheet: -0.79 (0.43), residues: 134 loop : -0.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.014 0.002 TYR A 498 PHE 0.022 0.002 PHE A 261 TRP 0.006 0.002 TRP A 9 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.31 (11748) covalent geometry : angle 0.62143 / 0.33 (15868) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 3.26484 / 1.73 ( 4) hydrogen bonds : bond 0.04316 / 2.86 ( 517) hydrogen bonds : angle 5.46413 / 3.68 ( 1497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8460 (t70) cc_final: 0.8257 (t-90) REVERT: A 95 MET cc_start: 0.8542 (tpp) cc_final: 0.8309 (mmm) REVERT: A 316 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: A 453 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8414 (ttt-90) REVERT: A 545 ASN cc_start: 0.8634 (m-40) cc_final: 0.8267 (m-40) REVERT: A 632 MET cc_start: 0.9011 (mtt) cc_final: 0.8404 (mtt) REVERT: A 658 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 660 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: B 11 GLN cc_start: 0.6914 (tt0) cc_final: 0.6445 (tm-30) REVERT: B 16 ILE cc_start: 0.8060 (mm) cc_final: 0.7845 (mm) REVERT: B 43 GLN cc_start: 0.7829 (mt0) cc_final: 0.7617 (mt0) REVERT: B 111 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7552 (mmtm) REVERT: B 240 MET cc_start: 0.3583 (OUTLIER) cc_final: 0.2910 (ppp) REVERT: B 309 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 384 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8178 (pp20) REVERT: B 393 SER cc_start: 0.8923 (t) cc_final: 0.8659 (t) outliers start: 42 outliers final: 23 residues processed: 178 average time/residue: 0.5494 time to fit residues: 105.8607 Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137842 restraints weight = 11884.480| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.49 r_work: 0.3485 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11750 Z= 0.142 Angle : 0.508 6.957 15872 Z= 0.269 Chirality : 0.041 0.160 1686 Planarity : 0.003 0.040 2014 Dihedral : 9.203 131.265 1696 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.52 % Allowed : 21.92 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1382 helix: 0.92 (0.20), residues: 662 sheet: -0.88 (0.42), residues: 134 loop : -0.03 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 331 TYR 0.013 0.001 TYR B 574 PHE 0.018 0.002 PHE B 100 TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (11748) covalent geometry : angle 0.50625 / 0.27 (15868) SS BOND : bond 0.00424 / 0.22 ( 2) SS BOND : angle 2.76298 / 1.44 ( 4) hydrogen bonds : bond 0.03399 / 2.27 ( 517) hydrogen bonds : angle 5.08656 / 3.43 ( 1497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7238 (mp0) REVERT: A 144 MET cc_start: 0.8718 (mtm) cc_final: 0.8489 (mtm) REVERT: A 316 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 453 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8437 (ttt-90) REVERT: A 545 ASN cc_start: 0.8631 (m-40) cc_final: 0.8292 (m-40) REVERT: A 632 MET cc_start: 0.9052 (mtt) cc_final: 0.8399 (mtt) REVERT: A 658 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 11 GLN cc_start: 0.6805 (tt0) cc_final: 0.6470 (tt0) REVERT: B 43 GLN cc_start: 0.7806 (mt0) cc_final: 0.7564 (mt0) REVERT: B 131 ASN cc_start: 0.8184 (t0) cc_final: 0.7833 (t0) REVERT: B 240 MET cc_start: 0.3768 (OUTLIER) cc_final: 0.3237 (ppp) REVERT: B 341 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7408 (mtpt) REVERT: B 348 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7939 (ptp) REVERT: B 384 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8017 (pp20) REVERT: B 393 SER cc_start: 0.8819 (t) cc_final: 0.8556 (t) REVERT: B 421 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: B 658 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7968 (mt) outliers start: 31 outliers final: 12 residues processed: 168 average time/residue: 0.5263 time to fit residues: 96.0676 Evaluate side-chains 164 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 410 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119499 restraints weight = 11495.704| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.39 r_work: 0.3189 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11750 Z= 0.286 Angle : 0.604 7.730 15872 Z= 0.317 Chirality : 0.045 0.156 1686 Planarity : 0.004 0.043 2014 Dihedral : 9.462 130.536 1696 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.60 % Allowed : 21.92 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.16 (0.22), residues: 1382 helix: 0.64 (0.20), residues: 662 sheet: -0.90 (0.43), residues: 134 loop : -0.09 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 331 TYR 0.014 0.002 TYR A 498 PHE 0.021 0.002 PHE B 74 TRP 0.006 0.002 TRP A 9 HIS 0.004 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (11748) covalent geometry : angle 0.60233 / 0.32 (15868) SS BOND : bond 0.00101 / 0.05 ( 2) SS BOND : angle 3.10962 / 1.64 ( 4) hydrogen bonds : bond 0.04148 / 2.76 ( 517) hydrogen bonds : angle 5.39151 / 3.63 ( 1497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7257 (mp0) REVERT: A 316 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 328 ASP cc_start: 0.7980 (m-30) cc_final: 0.7684 (m-30) REVERT: A 453 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8416 (ttt-90) REVERT: A 545 ASN cc_start: 0.8620 (m-40) cc_final: 0.8246 (m-40) REVERT: A 632 MET cc_start: 0.9015 (mtt) cc_final: 0.8401 (mtt) REVERT: A 658 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8330 (mp) REVERT: B 11 GLN cc_start: 0.6784 (tt0) cc_final: 0.6331 (tm-30) REVERT: B 43 GLN cc_start: 0.7810 (mt0) cc_final: 0.7572 (mt0) REVERT: B 240 MET cc_start: 0.3544 (OUTLIER) cc_final: 0.2849 (ppp) REVERT: B 322 MET cc_start: 0.8849 (mmm) cc_final: 0.8478 (mmm) REVERT: B 384 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: B 393 SER cc_start: 0.8894 (t) cc_final: 0.8615 (t) REVERT: B 658 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7908 (mt) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.6006 time to fit residues: 104.4632 Evaluate side-chains 161 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123897 restraints weight = 11358.904| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.35 r_work: 0.3255 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11750 Z= 0.140 Angle : 0.509 6.752 15872 Z= 0.270 Chirality : 0.041 0.158 1686 Planarity : 0.003 0.041 2014 Dihedral : 9.138 131.190 1696 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.27 % Allowed : 22.40 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1382 helix: 0.95 (0.20), residues: 660 sheet: -0.94 (0.42), residues: 134 loop : -0.05 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 331 TYR 0.013 0.001 TYR B 574 PHE 0.018 0.002 PHE B 100 TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11748) covalent geometry : angle 0.50726 / 0.27 (15868) SS BOND : bond 0.00198 / 0.10 ( 2) SS BOND : angle 2.84245 / 1.48 ( 4) hydrogen bonds : bond 0.03421 / 2.28 ( 517) hydrogen bonds : angle 5.07584 / 3.42 ( 1497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7183 (mp0) REVERT: A 316 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: A 328 ASP cc_start: 0.7784 (m-30) cc_final: 0.7470 (m-30) REVERT: A 453 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: A 545 ASN cc_start: 0.8599 (m-40) cc_final: 0.8265 (m-40) REVERT: A 658 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 11 GLN cc_start: 0.6689 (tt0) cc_final: 0.6312 (tm-30) REVERT: B 43 GLN cc_start: 0.7725 (mt0) cc_final: 0.7468 (mt0) REVERT: B 131 ASN cc_start: 0.8165 (t0) cc_final: 0.7785 (t0) REVERT: B 232 ASN cc_start: 0.8066 (m-40) cc_final: 0.7854 (t0) REVERT: B 240 MET cc_start: 0.3619 (OUTLIER) cc_final: 0.3104 (ppp) REVERT: B 341 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7271 (mtpt) REVERT: B 348 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7837 (ptp) REVERT: B 384 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7929 (pp20) REVERT: B 393 SER cc_start: 0.8789 (t) cc_final: 0.8520 (t) REVERT: B 421 GLU cc_start: 0.8143 (pt0) cc_final: 0.7785 (pp20) REVERT: B 658 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7877 (mt) outliers start: 28 outliers final: 14 residues processed: 171 average time/residue: 0.5448 time to fit residues: 101.4185 Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113522 restraints weight = 12167.040| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.57 r_work: 0.3122 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11750 Z= 0.177 Angle : 0.538 8.068 15872 Z= 0.283 Chirality : 0.042 0.156 1686 Planarity : 0.003 0.042 2014 Dihedral : 9.131 131.237 1696 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.11 % Allowed : 22.24 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.22), residues: 1382 helix: 0.90 (0.20), residues: 662 sheet: -1.02 (0.42), residues: 134 loop : -0.06 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 331 TYR 0.012 0.001 TYR A 498 PHE 0.024 0.002 PHE B 98 TRP 0.005 0.001 TRP A 9 HIS 0.007 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11748) covalent geometry : angle 0.53500 / 0.28 (15868) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 3.41877 / 1.81 ( 4) hydrogen bonds : bond 0.03646 / 2.43 ( 517) hydrogen bonds : angle 5.12635 / 3.45 ( 1497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6814 (mp0) REVERT: A 316 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 328 ASP cc_start: 0.7679 (m-30) cc_final: 0.7369 (m-30) REVERT: A 453 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7812 (ttt-90) REVERT: A 545 ASN cc_start: 0.8208 (m-40) cc_final: 0.7810 (m-40) REVERT: A 632 MET cc_start: 0.8721 (mtt) cc_final: 0.8146 (mtt) REVERT: A 658 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7836 (mp) REVERT: B 11 GLN cc_start: 0.6120 (tt0) cc_final: 0.5474 (mt0) REVERT: B 43 GLN cc_start: 0.7539 (mt0) cc_final: 0.7302 (mt0) REVERT: B 240 MET cc_start: 0.3446 (OUTLIER) cc_final: 0.2768 (ppp) REVERT: B 341 LYS cc_start: 0.7180 (mmmm) cc_final: 0.6455 (mtpm) REVERT: B 384 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7952 (pp20) REVERT: B 393 SER cc_start: 0.8468 (t) cc_final: 0.8109 (t) REVERT: B 421 GLU cc_start: 0.7874 (pt0) cc_final: 0.7528 (pt0) REVERT: B 658 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7356 (mt) outliers start: 26 outliers final: 17 residues processed: 159 average time/residue: 0.5496 time to fit residues: 94.9431 Evaluate side-chains 158 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 114 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118048 restraints weight = 12132.413| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.63 r_work: 0.3189 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.125 Angle : 0.497 7.612 15872 Z= 0.263 Chirality : 0.041 0.157 1686 Planarity : 0.003 0.040 2014 Dihedral : 8.771 131.938 1696 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.87 % Allowed : 22.65 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.52 (0.22), residues: 1382 helix: 1.10 (0.20), residues: 662 sheet: -1.08 (0.41), residues: 134 loop : -0.03 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 331 TYR 0.012 0.001 TYR B 574 PHE 0.019 0.001 PHE B 74 TRP 0.005 0.001 TRP A 9 HIS 0.007 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11748) covalent geometry : angle 0.49513 / 0.26 (15868) SS BOND : bond 0.00244 / 0.12 ( 2) SS BOND : angle 2.92505 / 1.54 ( 4) hydrogen bonds : bond 0.03256 / 2.17 ( 517) hydrogen bonds : angle 4.91691 / 3.32 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.76 seconds wall clock time: 65 minutes 19.13 seconds (3919.13 seconds total)