Starting phenix.real_space_refine on Sat Aug 23 10:19:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxc_45004/08_2025/9bxc_45004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxc_45004/08_2025/9bxc_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_45004/08_2025/9bxc_45004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxc_45004/08_2025/9bxc_45004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxc_45004/08_2025/9bxc_45004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxc_45004/08_2025/9bxc_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-2.0-5787/lib/python3.9/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: 2.87, per 1000 atoms: 0.25 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: 0.83 Conformation dependent library (CDL) restraints added in 563.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.42 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: 2.09 Time building geometry restraints manager: 1.12 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=" CB PRO D 314 " pdb=" CG PRO D 314 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB CYS A 170 " pdb=" SG CYS A 170 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB ASP A 215 " pdb=" CG ASP A 215 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.19e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 15539 1.51 - 3.02: 255 3.02 - 4.52: 51 4.52 - 6.03: 20 6.03 - 7.54: 3 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=" 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=" 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 angle pdb=" C VAL C 312 " pdb=" CA VAL C 312 " pdb=" CB VAL C 312 " ideal model delta sigma weight residual 111.29 116.82 -5.53 1.64e+00 3.72e-01 1.14e+01 angle pdb=" C GLN B 239 " pdb=" N MET B 240 " pdb=" CA MET B 240 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 ... (remaining 15863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 6597 29.73 - 59.46: 458 59.46 - 89.19: 38 89.19 - 118.93: 3 118.93 - 148.66: 4 Dihedral angle restraints: 7100 sinusoidal: 2976 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=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 153.03 148.66 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 156.37 145.31 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1054 0.031 - 0.063: 455 0.063 - 0.094: 114 0.094 - 0.126: 57 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: 0.02 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: 1.540 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.900 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.003 0.084 11750 Z= 0.120 Angle : 0.538 7.538 15872 Z= 0.287 Chirality : 0.040 0.157 1686 Planarity : 0.003 0.040 2014 Dihedral : 18.609 148.658 4442 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 aren 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 covalent geometry : bond 0.00273 (11748) covalent geometry : angle 0.53571 (15868) SS BOND : bond 0.00403 ( 2) SS BOND : angle 2.90084 ( 4) hydrogen bonds : bond 0.15268 ( 517) hydrogen bonds : angle 6.76712 ( 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 : 0.313 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: 0.5950 time to fit residues: 110.4666 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 : 0.373 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 329 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 = 0.3631 r_free = 0.3631 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118791 restraints weight = 11531.778| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.37 r_work: 0.3194 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11750 Z= 0.283 Angle : 0.630 7.198 15872 Z= 0.328 Chirality : 0.046 0.169 1686 Planarity : 0.004 0.040 2014 Dihedral : 12.742 161.412 1663 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.73 % Allowed : 19.16 % Favored : 77.11 % 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 aren not related in a simple way. whole: 0.40 (0.22), residues: 1382 helix: 0.73 (0.20), residues: 658 sheet: -0.63 (0.42), residues: 134 loop : 0.15 (0.25), residues: 590 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 0.021 0.002 PHE A 37 TRP 0.006 0.002 TRP A 9 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00667 (11748) covalent geometry : angle 0.62680 (15868) SS BOND : bond 0.00199 ( 2) SS BOND : angle 3.78305 ( 4) hydrogen bonds : bond 0.04521 ( 517) hydrogen bonds : angle 5.62932 ( 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 193 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: A 75 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7229 (mp0) REVERT: A 214 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6109 (mtmm) REVERT: A 316 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 317 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8614 (mtp) REVERT: A 658 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 11 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: B 15 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: B 30 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7543 (tttm) REVERT: B 43 GLN cc_start: 0.7769 (mt0) cc_final: 0.7543 (mt0) REVERT: B 111 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7626 (mmtm) REVERT: B 240 MET cc_start: 0.3800 (OUTLIER) cc_final: 0.3174 (ppp) REVERT: B 384 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8150 (pp20) REVERT: B 658 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8060 (mt) outliers start: 46 outliers final: 21 residues processed: 178 average time/residue: 0.5555 time to fit residues: 107.0300 Evaluate side-chains 173 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 214 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 317 MET 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 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 30 LYS 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 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 570 MET 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: 3.9990 chunk 136 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 94 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN A 320 ASN A 329 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114481 restraints weight = 12333.959| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.47 r_work: 0.3092 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1206 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= 0.130 Angle : 0.526 11.823 15872 Z= 0.273 Chirality : 0.041 0.168 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.959 150.827 1659 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.52 % Allowed : 20.94 % Favored : 76.54 % 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 aren not related in a simple way. whole: 0.64 (0.22), residues: 1382 helix: 1.03 (0.20), residues: 660 sheet: -0.58 (0.43), residues: 134 loop : 0.13 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00295 (11748) covalent geometry : angle 0.51989 (15868) SS BOND : bond 0.00122 ( 2) SS BOND : angle 4.94982 ( 4) hydrogen bonds : bond 0.03450 ( 517) hydrogen bonds : angle 5.09414 ( 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.288 Fit side-chains REVERT: A 75 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7005 (mp0) REVERT: A 232 ASN cc_start: 0.8399 (m110) cc_final: 0.8099 (m-40) REVERT: A 317 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8477 (mtp) REVERT: A 658 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 11 GLN cc_start: 0.6434 (tt0) cc_final: 0.6132 (tt0) REVERT: B 15 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: B 43 GLN cc_start: 0.7677 (mt0) cc_final: 0.7414 (mt0) REVERT: B 240 MET cc_start: 0.3650 (ppp) cc_final: 0.3066 (ppp) REVERT: B 348 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7618 (ptp) REVERT: B 384 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7969 (pp20) REVERT: B 393 SER cc_start: 0.8625 (t) cc_final: 0.8347 (t) REVERT: B 658 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7680 (mt) outliers start: 31 outliers final: 9 residues processed: 173 average time/residue: 0.4916 time to fit residues: 92.6305 Evaluate side-chains 158 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 446 ARG 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: 0.9980 chunk 20 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 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 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 = 0.3657 r_free = 0.3657 target = 0.146623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120687 restraints weight = 11518.076| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.40 r_work: 0.3197 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11750 Z= 0.254 Angle : 0.594 9.430 15872 Z= 0.308 Chirality : 0.044 0.163 1686 Planarity : 0.004 0.042 2014 Dihedral : 12.111 161.304 1648 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.65 % Allowed : 19.56 % Favored : 76.79 % 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 aren not related in a simple way. whole: 0.34 (0.22), residues: 1382 helix: 0.76 (0.20), residues: 660 sheet: -0.72 (0.43), residues: 134 loop : 0.01 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 331 TYR 0.013 0.002 TYR A 498 PHE 0.021 0.002 PHE A 100 TRP 0.006 0.001 TRP A 9 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00599 (11748) covalent geometry : angle 0.58967 (15868) SS BOND : bond 0.00445 ( 2) SS BOND : angle 4.59670 ( 4) hydrogen bonds : bond 0.04099 ( 517) hydrogen bonds : angle 5.33364 ( 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 190 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7150 (mp0) REVERT: A 316 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: A 362 ASP cc_start: 0.8081 (m-30) cc_final: 0.7875 (m-30) REVERT: A 545 ASN cc_start: 0.8583 (m-40) cc_final: 0.8246 (m-40) REVERT: A 632 MET cc_start: 0.8996 (mtt) cc_final: 0.8256 (mtt) REVERT: A 658 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 660 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: B 11 GLN cc_start: 0.6857 (tt0) cc_final: 0.6455 (tt0) REVERT: B 15 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: B 43 GLN cc_start: 0.7736 (mt0) cc_final: 0.7526 (mt0) REVERT: B 232 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7998 (t0) REVERT: B 240 MET cc_start: 0.3627 (OUTLIER) cc_final: 0.2995 (ppp) REVERT: B 309 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: B 384 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: B 393 SER cc_start: 0.8882 (t) cc_final: 0.8615 (t) REVERT: B 658 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7935 (mt) outliers start: 45 outliers final: 20 residues processed: 172 average time/residue: 0.5292 time to fit residues: 98.4617 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 348 MET 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 611 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 A residue 684 TYR 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 232 ASN 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 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: 1.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 320 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 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 = 0.3556 r_free = 0.3556 target = 0.141248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115707 restraints weight = 12245.562| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.44 r_work: 0.3144 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1395 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= 0.119 Angle : 0.496 7.201 15872 Z= 0.259 Chirality : 0.040 0.163 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.593 148.868 1648 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.52 % Allowed : 21.02 % Favored : 76.46 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1382 helix: 1.07 (0.20), residues: 662 sheet: -0.87 (0.41), residues: 142 loop : 0.11 (0.25), residues: 578 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 covalent geometry : bond 0.00269 (11748) covalent geometry : angle 0.49407 (15868) SS BOND : bond 0.00234 ( 2) SS BOND : angle 2.85692 ( 4) hydrogen bonds : bond 0.03206 ( 517) hydrogen bonds : angle 4.94488 ( 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 189 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.498 Fit side-chains REVERT: A 75 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7027 (mp0) REVERT: A 144 MET cc_start: 0.8683 (mtm) cc_final: 0.8470 (mtm) REVERT: A 235 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7220 (mtm110) REVERT: A 316 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 545 ASN cc_start: 0.8381 (m-40) cc_final: 0.8063 (m-40) REVERT: A 610 LYS cc_start: 0.7335 (tttt) cc_final: 0.7129 (tptt) REVERT: A 640 MET cc_start: 0.8996 (tpp) cc_final: 0.8760 (tpp) REVERT: A 658 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 11 GLN cc_start: 0.6370 (tt0) cc_final: 0.6086 (tt0) REVERT: B 15 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: B 16 ILE cc_start: 0.7831 (mm) cc_final: 0.7615 (mm) REVERT: B 43 GLN cc_start: 0.7670 (mt0) cc_final: 0.7407 (mt0) REVERT: B 240 MET cc_start: 0.3463 (OUTLIER) cc_final: 0.2962 (ppp) REVERT: B 341 LYS cc_start: 0.7549 (mmmm) cc_final: 0.6863 (mtpt) REVERT: B 348 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7590 (ptp) REVERT: B 393 SER cc_start: 0.8633 (t) cc_final: 0.8331 (t) REVERT: B 421 GLU cc_start: 0.8113 (pt0) cc_final: 0.7773 (pp20) REVERT: B 427 LYS cc_start: 0.7822 (mptt) cc_final: 0.7021 (ptmm) REVERT: B 662 MET cc_start: 0.7854 (ptp) cc_final: 0.7420 (ptp) outliers start: 31 outliers final: 10 residues processed: 176 average time/residue: 0.7038 time to fit residues: 133.7783 Evaluate side-chains 164 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 141 VAL 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 541 GLU 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: 5.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3628 r_free = 0.3628 target = 0.143945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117991 restraints weight = 11564.133| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.40 r_work: 0.3109 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 11750 Z= 0.358 Angle : 0.666 8.292 15872 Z= 0.345 Chirality : 0.048 0.160 1686 Planarity : 0.004 0.044 2014 Dihedral : 12.502 170.769 1648 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.65 % Allowed : 20.70 % 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 aren not related in a simple way. whole: 0.07 (0.22), residues: 1382 helix: 0.55 (0.20), residues: 656 sheet: -0.83 (0.43), residues: 134 loop : -0.15 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 331 TYR 0.016 0.002 TYR B 307 PHE 0.026 0.003 PHE A 37 TRP 0.006 0.002 TRP A 9 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00850 (11748) covalent geometry : angle 0.66358 (15868) SS BOND : bond 0.00088 ( 2) SS BOND : angle 3.27351 ( 4) hydrogen bonds : bond 0.04476 ( 517) hydrogen bonds : angle 5.51799 ( 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 194 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 335 GLU cc_start: 0.7652 (pt0) cc_final: 0.7272 (pt0) REVERT: A 453 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8428 (ttt-90) REVERT: A 545 ASN cc_start: 0.8627 (m-40) cc_final: 0.8255 (m-40) REVERT: A 658 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 660 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: B 11 GLN cc_start: 0.6861 (tt0) cc_final: 0.6484 (tt0) REVERT: B 15 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: B 43 GLN cc_start: 0.7841 (mt0) cc_final: 0.7634 (mt0) REVERT: B 111 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7558 (mmtm) REVERT: B 214 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6706 (ttpp) REVERT: B 240 MET cc_start: 0.3657 (OUTLIER) cc_final: 0.2975 (ppp) REVERT: B 309 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: B 384 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: B 393 SER cc_start: 0.8923 (t) cc_final: 0.8656 (t) REVERT: B 658 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 662 MET cc_start: 0.8110 (ptp) cc_final: 0.7301 (ptp) outliers start: 45 outliers final: 19 residues processed: 176 average time/residue: 0.6600 time to fit residues: 125.5122 Evaluate side-chains 172 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 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 15 GLU 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 214 LYS 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 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: 2.9990 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 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 410 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 = 0.3915 r_free = 0.3915 target = 0.162930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138119 restraints weight = 11901.458| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.49 r_work: 0.3485 rms_B_bonded: 2.31 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: 0.8077 moved from start: 0.1523 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= 0.134 Angle : 0.520 6.765 15872 Z= 0.271 Chirality : 0.041 0.159 1686 Planarity : 0.003 0.040 2014 Dihedral : 11.811 156.665 1648 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 21.83 % Favored : 75.73 % 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 aren not related in a simple way. whole: 0.36 (0.22), residues: 1382 helix: 0.93 (0.20), residues: 648 sheet: -0.82 (0.43), residues: 134 loop : -0.14 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 331 TYR 0.013 0.001 TYR B 574 PHE 0.017 0.002 PHE B 100 TRP 0.007 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00306 (11748) covalent geometry : angle 0.51817 (15868) SS BOND : bond 0.00302 ( 2) SS BOND : angle 2.71005 ( 4) hydrogen bonds : bond 0.03378 ( 517) hydrogen bonds : angle 5.07424 ( 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 180 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7269 (mp0) REVERT: A 316 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 328 ASP cc_start: 0.7860 (m-30) cc_final: 0.7598 (m-30) REVERT: A 335 GLU cc_start: 0.7448 (pt0) cc_final: 0.7124 (pt0) REVERT: A 362 ASP cc_start: 0.8068 (m-30) cc_final: 0.7851 (m-30) REVERT: A 453 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8431 (ttt-90) REVERT: A 545 ASN cc_start: 0.8633 (m-40) cc_final: 0.8314 (m-40) REVERT: A 658 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 11 GLN cc_start: 0.6807 (tt0) cc_final: 0.6481 (tt0) REVERT: B 43 GLN cc_start: 0.7795 (mt0) cc_final: 0.7561 (mt0) REVERT: B 240 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.3280 (ppp) REVERT: B 348 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7941 (ptp) REVERT: B 384 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: B 393 SER cc_start: 0.8828 (t) cc_final: 0.8560 (t) REVERT: B 421 GLU cc_start: 0.8152 (pt0) cc_final: 0.7805 (pp20) REVERT: B 658 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7735 (mt) outliers start: 30 outliers final: 11 residues processed: 168 average time/residue: 0.6176 time to fit residues: 112.3048 Evaluate side-chains 162 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 141 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 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: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 232 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3628 r_free = 0.3628 target = 0.144109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118957 restraints weight = 11597.807| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.37 r_work: 0.3179 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11750 Z= 0.271 Angle : 0.615 7.687 15872 Z= 0.318 Chirality : 0.045 0.155 1686 Planarity : 0.004 0.043 2014 Dihedral : 12.181 166.002 1648 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.44 % Allowed : 22.40 % Favored : 75.16 % 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 aren not related in a simple way. whole: 0.15 (0.22), residues: 1382 helix: 0.66 (0.20), residues: 662 sheet: -0.91 (0.43), residues: 134 loop : -0.13 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 331 TYR 0.014 0.002 TYR A 498 PHE 0.022 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 covalent geometry : bond 0.00642 (11748) covalent geometry : angle 0.61311 (15868) SS BOND : bond 0.00120 ( 2) SS BOND : angle 3.02874 ( 4) hydrogen bonds : bond 0.04095 ( 517) hydrogen bonds : angle 5.35377 ( 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 174 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7253 (mp0) REVERT: A 95 MET cc_start: 0.8590 (tpp) cc_final: 0.8260 (tpp) REVERT: A 316 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: A 328 ASP cc_start: 0.7952 (m-30) cc_final: 0.7647 (m-30) REVERT: A 329 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8410 (t0) REVERT: A 453 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8387 (ttt-90) REVERT: A 545 ASN cc_start: 0.8613 (m-40) cc_final: 0.8226 (m-40) REVERT: A 658 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 11 GLN cc_start: 0.6787 (tt0) cc_final: 0.6443 (tt0) REVERT: B 43 GLN cc_start: 0.7796 (mt0) cc_final: 0.7554 (mt0) REVERT: B 240 MET cc_start: 0.3717 (OUTLIER) cc_final: 0.3094 (ppp) REVERT: B 309 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 384 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: B 393 SER cc_start: 0.8903 (t) cc_final: 0.8624 (t) REVERT: B 658 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7879 (mt) REVERT: B 662 MET cc_start: 0.8090 (ptp) cc_final: 0.7348 (ptp) outliers start: 30 outliers final: 16 residues processed: 163 average time/residue: 0.6329 time to fit residues: 111.7450 Evaluate side-chains 162 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 329 ASN 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 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 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: 0.9980 chunk 109 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 232 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3705 r_free = 0.3705 target = 0.151214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125840 restraints weight = 11257.945| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.38 r_work: 0.3260 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1558 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= 0.137 Angle : 0.526 6.757 15872 Z= 0.273 Chirality : 0.041 0.158 1686 Planarity : 0.003 0.041 2014 Dihedral : 11.659 155.092 1648 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 22.32 % 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 aren not related in a simple way. whole: 0.34 (0.22), residues: 1382 helix: 0.93 (0.20), residues: 650 sheet: -0.90 (0.43), residues: 134 loop : -0.16 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 331 TYR 0.012 0.001 TYR B 574 PHE 0.017 0.002 PHE B 74 TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00316 (11748) covalent geometry : angle 0.52464 (15868) SS BOND : bond 0.00447 ( 2) SS BOND : angle 2.68429 ( 4) hydrogen bonds : bond 0.03365 ( 517) hydrogen bonds : angle 5.04556 ( 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 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.489 Fit side-chains REVERT: A 75 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7178 (mp0) REVERT: A 144 MET cc_start: 0.8685 (mtm) cc_final: 0.8441 (mtm) REVERT: A 316 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 317 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8469 (mtp) REVERT: A 328 ASP cc_start: 0.7723 (m-30) cc_final: 0.7447 (m-30) REVERT: A 453 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8369 (ttt-90) REVERT: A 545 ASN cc_start: 0.8647 (m-40) cc_final: 0.8318 (m-40) REVERT: A 658 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 11 GLN cc_start: 0.6681 (tt0) cc_final: 0.6298 (tm-30) REVERT: B 43 GLN cc_start: 0.7741 (mt0) cc_final: 0.7479 (mt0) REVERT: B 240 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3175 (ppp) REVERT: B 348 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7819 (ptp) REVERT: B 384 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7928 (pp20) REVERT: B 393 SER cc_start: 0.8797 (t) cc_final: 0.8527 (t) REVERT: B 421 GLU cc_start: 0.8183 (pt0) cc_final: 0.7809 (pp20) REVERT: B 658 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7667 (mt) outliers start: 26 outliers final: 12 residues processed: 168 average time/residue: 0.6214 time to fit residues: 113.4387 Evaluate side-chains 160 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 317 MET 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 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: 1.9990 chunk 74 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114112 restraints weight = 12155.738| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.60 r_work: 0.3146 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11750 Z= 0.166 Angle : 0.552 8.601 15872 Z= 0.284 Chirality : 0.042 0.155 1686 Planarity : 0.003 0.041 2014 Dihedral : 11.634 157.337 1648 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.79 % Allowed : 22.16 % 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 aren not related in a simple way. whole: 0.38 (0.22), residues: 1382 helix: 0.93 (0.20), residues: 662 sheet: -0.98 (0.42), residues: 134 loop : -0.09 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 331 TYR 0.013 0.001 TYR A 612 PHE 0.025 0.002 PHE B 98 TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS B 568 Details of bonding type rmsd covalent geometry : bond 0.00387 (11748) covalent geometry : angle 0.54918 (15868) SS BOND : bond 0.00266 ( 2) SS BOND : angle 3.32949 ( 4) hydrogen bonds : bond 0.03531 ( 517) hydrogen bonds : angle 5.08303 ( 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 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6890 (mp0) REVERT: A 316 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 317 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8201 (mtp) REVERT: A 328 ASP cc_start: 0.7632 (m-30) cc_final: 0.7367 (m-30) REVERT: A 453 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7876 (ttt-90) REVERT: A 545 ASN cc_start: 0.8295 (m-40) cc_final: 0.7903 (m-40) REVERT: A 658 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 11 GLN cc_start: 0.6162 (tt0) cc_final: 0.5511 (mt0) REVERT: B 43 GLN cc_start: 0.7585 (mt0) cc_final: 0.7335 (mt0) REVERT: B 240 MET cc_start: 0.3451 (OUTLIER) cc_final: 0.2900 (ppp) REVERT: B 348 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7397 (ptp) REVERT: B 384 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7906 (pp20) REVERT: B 393 SER cc_start: 0.8540 (t) cc_final: 0.8195 (t) REVERT: B 658 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7215 (mt) outliers start: 22 outliers final: 13 residues processed: 162 average time/residue: 0.6008 time to fit residues: 105.5927 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 317 MET 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 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 51 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 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 ** 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 = 0.3556 r_free = 0.3556 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112605 restraints weight = 12208.150| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.60 r_work: 0.3114 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11750 Z= 0.184 Angle : 0.566 8.342 15872 Z= 0.291 Chirality : 0.042 0.155 1686 Planarity : 0.003 0.042 2014 Dihedral : 11.624 158.581 1648 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.19 % Allowed : 21.83 % Favored : 75.97 % 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 aren not related in a simple way. whole: 0.33 (0.22), residues: 1382 helix: 0.89 (0.20), residues: 662 sheet: -1.04 (0.42), residues: 134 loop : -0.10 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 331 TYR 0.014 0.001 TYR A 612 PHE 0.023 0.002 PHE B 74 TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS B 568 Details of bonding type rmsd covalent geometry : bond 0.00431 (11748) covalent geometry : angle 0.56387 (15868) SS BOND : bond 0.00202 ( 2) SS BOND : angle 3.27031 ( 4) hydrogen bonds : bond 0.03654 ( 517) hydrogen bonds : angle 5.14394 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.17 seconds wall clock time: 67 minutes 27.96 seconds (4047.96 seconds total)