Starting phenix.real_space_refine on Tue Jun 10 06:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxc_45004/06_2025/9bxc_45004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxc_45004/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxc_45004/06_2025/9bxc_45004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxc_45004/06_2025/9bxc_45004.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxc_45004/06_2025/9bxc_45004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxc_45004/06_2025/9bxc_45004.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.47, per 1000 atoms: 0.65 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.42 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: 3.57 Time building geometry restraints manager: 3.33 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.920 Find NCS groups from input model: 0.510 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- 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 : 11.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (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 TRP 0.006 0.001 TRP B 9 HIS 0.004 0.001 HIS B 255 PHE 0.015 0.001 PHE A 100 TYR 0.008 0.001 TYR A 471 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.15268 ( 517) hydrogen bonds : angle 6.76712 ( 1497) SS BOND : bond 0.00403 ( 2) SS BOND : angle 2.90084 ( 4) covalent geometry : bond 0.00273 (11748) covalent geometry : angle 0.53571 (15868) *********************** 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 : 1.291 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: 1.2639 time to fit residues: 235.9375 Evaluate side-chains 153 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 232 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121256 restraints weight = 11273.563| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.39 r_work: 0.3193 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11750 Z= 0.246 Angle : 0.602 6.633 15872 Z= 0.315 Chirality : 0.045 0.168 1686 Planarity : 0.004 0.040 2014 Dihedral : 12.591 157.734 1663 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.81 % Allowed : 19.24 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1382 helix: 0.82 (0.20), residues: 660 sheet: -0.63 (0.42), residues: 134 loop : 0.16 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.007 0.001 HIS A 304 PHE 0.020 0.002 PHE A 100 TYR 0.015 0.002 TYR B 574 ARG 0.008 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 517) hydrogen bonds : angle 5.53994 ( 1497) SS BOND : bond 0.00147 ( 2) SS BOND : angle 3.53156 ( 4) covalent geometry : bond 0.00578 (11748) covalent geometry : angle 0.59948 (15868) *********************** 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 198 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: A 75 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7274 (mp0) REVERT: A 316 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 632 MET cc_start: 0.9001 (mtt) cc_final: 0.8260 (mtt) REVERT: A 658 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8400 (mp) REVERT: B 11 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: B 15 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: B 30 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7535 (tttm) REVERT: B 43 GLN cc_start: 0.7794 (mt0) cc_final: 0.7561 (mt0) REVERT: B 111 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7628 (mmtm) REVERT: B 240 MET cc_start: 0.3747 (OUTLIER) cc_final: 0.3151 (ppp) REVERT: B 341 LYS cc_start: 0.7862 (mmmm) cc_final: 0.7299 (mtpm) REVERT: B 384 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8107 (pp20) REVERT: B 658 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8130 (mt) outliers start: 47 outliers final: 23 residues processed: 183 average time/residue: 1.2359 time to fit residues: 246.1068 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 : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 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 321 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 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 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113809 restraints weight = 12262.232| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.51 r_work: 0.3137 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11750 Z= 0.148 Angle : 0.536 12.331 15872 Z= 0.278 Chirality : 0.041 0.169 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.984 151.715 1659 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.84 % Allowed : 20.45 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1382 helix: 1.01 (0.20), residues: 660 sheet: -0.55 (0.43), residues: 134 loop : 0.13 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 PHE 0.018 0.002 PHE B 100 TYR 0.011 0.001 TYR B 574 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 517) hydrogen bonds : angle 5.11852 ( 1497) SS BOND : bond 0.00440 ( 2) SS BOND : angle 5.02988 ( 4) covalent geometry : bond 0.00339 (11748) covalent geometry : angle 0.52974 (15868) *********************** 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 196 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.353 Fit side-chains REVERT: A 75 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6964 (mp0) REVERT: A 316 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 632 MET cc_start: 0.8946 (mtt) cc_final: 0.8241 (mtt) REVERT: A 658 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8219 (mp) REVERT: B 11 GLN cc_start: 0.6561 (tt0) cc_final: 0.6245 (tt0) REVERT: B 15 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: B 43 GLN cc_start: 0.7661 (mt0) cc_final: 0.7429 (mt0) REVERT: B 169 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 240 MET cc_start: 0.3646 (ppp) cc_final: 0.3060 (ppp) REVERT: B 341 LYS cc_start: 0.7612 (mmmm) cc_final: 0.6960 (mtpt) REVERT: B 348 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7678 (ptp) REVERT: B 384 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: B 393 SER cc_start: 0.8721 (t) cc_final: 0.8443 (t) REVERT: B 658 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (mt) outliers start: 35 outliers final: 9 residues processed: 180 average time/residue: 1.4540 time to fit residues: 285.6365 Evaluate side-chains 161 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 446 ARG Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 348 MET 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 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** 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 = 0.3570 r_free = 0.3570 target = 0.142405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116673 restraints weight = 12160.126| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.43 r_work: 0.3118 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11750 Z= 0.120 Angle : 0.498 8.585 15872 Z= 0.259 Chirality : 0.040 0.167 1686 Planarity : 0.003 0.037 2014 Dihedral : 11.490 148.028 1648 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.84 % Allowed : 20.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1382 helix: 1.18 (0.20), residues: 662 sheet: -0.57 (0.44), residues: 134 loop : 0.12 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.005 0.001 HIS B 438 PHE 0.016 0.001 PHE A 100 TYR 0.010 0.001 TYR B 574 ARG 0.008 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 517) hydrogen bonds : angle 4.87763 ( 1497) SS BOND : bond 0.00458 ( 2) SS BOND : angle 3.68334 ( 4) covalent geometry : bond 0.00270 (11748) covalent geometry : angle 0.49470 (15868) *********************** 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 192 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 2.375 Fit side-chains REVERT: A 75 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7021 (mp0) REVERT: A 316 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 545 ASN cc_start: 0.8488 (m-40) cc_final: 0.8152 (m-40) REVERT: A 632 MET cc_start: 0.8926 (mtt) cc_final: 0.8215 (mtt) REVERT: A 658 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 11 GLN cc_start: 0.6427 (tt0) cc_final: 0.6126 (tt0) REVERT: B 15 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: B 43 GLN cc_start: 0.7643 (mt0) cc_final: 0.7398 (mt0) REVERT: B 240 MET cc_start: 0.3550 (OUTLIER) cc_final: 0.2895 (ppp) REVERT: B 348 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7631 (ptp) REVERT: B 393 SER cc_start: 0.8710 (t) cc_final: 0.8412 (t) REVERT: B 421 GLU cc_start: 0.8161 (pt0) cc_final: 0.7794 (pp20) REVERT: B 662 MET cc_start: 0.7799 (ptp) cc_final: 0.7292 (ptp) outliers start: 35 outliers final: 9 residues processed: 178 average time/residue: 1.7987 time to fit residues: 344.7249 Evaluate side-chains 159 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 537 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 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 = 0.3657 r_free = 0.3657 target = 0.146845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120863 restraints weight = 11320.228| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.39 r_work: 0.3203 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1529 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= 0.249 Angle : 0.592 8.091 15872 Z= 0.307 Chirality : 0.044 0.161 1686 Planarity : 0.004 0.041 2014 Dihedral : 11.991 161.517 1644 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.41 % Allowed : 20.54 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1382 helix: 0.85 (0.20), residues: 662 sheet: -0.76 (0.43), residues: 134 loop : 0.03 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.006 0.001 HIS A 304 PHE 0.021 0.002 PHE A 100 TYR 0.015 0.002 TYR A 498 ARG 0.006 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 517) hydrogen bonds : angle 5.27305 ( 1497) SS BOND : bond 0.00299 ( 2) SS BOND : angle 3.78418 ( 4) covalent geometry : bond 0.00587 (11748) covalent geometry : angle 0.58911 (15868) *********************** 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 190 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7168 (mp0) REVERT: A 316 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 545 ASN cc_start: 0.8594 (m-40) cc_final: 0.8235 (m-40) REVERT: A 632 MET cc_start: 0.9017 (mtt) cc_final: 0.8373 (mtt) REVERT: A 658 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 660 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: B 11 GLN cc_start: 0.6905 (tt0) cc_final: 0.6538 (tt0) REVERT: B 15 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: B 43 GLN cc_start: 0.7795 (mt0) cc_final: 0.7566 (mt0) REVERT: B 131 ASN cc_start: 0.8129 (t0) cc_final: 0.7835 (t0) REVERT: B 240 MET cc_start: 0.3731 (OUTLIER) cc_final: 0.3078 (ppp) REVERT: B 309 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 322 MET cc_start: 0.8779 (mmm) cc_final: 0.8366 (mmm) REVERT: B 384 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8110 (pp20) REVERT: B 393 SER cc_start: 0.8913 (t) cc_final: 0.8642 (t) REVERT: B 658 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7810 (mt) REVERT: B 662 MET cc_start: 0.8065 (ptp) cc_final: 0.7173 (ptp) outliers start: 42 outliers final: 17 residues processed: 174 average time/residue: 1.5935 time to fit residues: 301.6285 Evaluate side-chains 170 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 256 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 367 VAL 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 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 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 445 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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 = 0.3910 r_free = 0.3910 target = 0.162332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137271 restraints weight = 11892.359| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.49 r_work: 0.3474 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11750 Z= 0.155 Angle : 0.524 7.298 15872 Z= 0.273 Chirality : 0.041 0.161 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.701 154.028 1644 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.52 % Allowed : 21.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1382 helix: 1.01 (0.20), residues: 662 sheet: -0.80 (0.43), residues: 134 loop : 0.04 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.018 0.002 PHE B 74 TYR 0.011 0.001 TYR B 574 ARG 0.010 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 517) hydrogen bonds : angle 5.06299 ( 1497) SS BOND : bond 0.00213 ( 2) SS BOND : angle 2.87991 ( 4) covalent geometry : bond 0.00360 (11748) covalent geometry : angle 0.52215 (15868) *********************** 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 184 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.482 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7342 (mp0) REVERT: A 144 MET cc_start: 0.8736 (mtm) cc_final: 0.8513 (mtm) REVERT: A 232 ASN cc_start: 0.8564 (m110) cc_final: 0.8223 (m-40) REVERT: A 316 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 335 GLU cc_start: 0.7480 (pt0) cc_final: 0.7134 (pt0) REVERT: A 545 ASN cc_start: 0.8682 (m-40) cc_final: 0.8340 (m-40) REVERT: A 632 MET cc_start: 0.9053 (mtt) cc_final: 0.8400 (mtt) REVERT: A 658 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 660 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6721 (m-30) REVERT: B 11 GLN cc_start: 0.6830 (tt0) cc_final: 0.6478 (tt0) REVERT: B 43 GLN cc_start: 0.7813 (mt0) cc_final: 0.7564 (mt0) REVERT: B 240 MET cc_start: 0.3630 (OUTLIER) cc_final: 0.3042 (ppp) REVERT: B 341 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7413 (mtpt) REVERT: B 384 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8013 (pp20) REVERT: B 393 SER cc_start: 0.8829 (t) cc_final: 0.8569 (t) REVERT: B 421 GLU cc_start: 0.8136 (pt0) cc_final: 0.7831 (pt0) REVERT: B 658 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7809 (mt) REVERT: B 662 MET cc_start: 0.8091 (ptp) cc_final: 0.7207 (ptp) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 1.2362 time to fit residues: 229.8610 Evaluate side-chains 167 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123195 restraints weight = 11555.664| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.40 r_work: 0.3216 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11750 Z= 0.185 Angle : 0.546 7.210 15872 Z= 0.283 Chirality : 0.042 0.157 1686 Planarity : 0.003 0.040 2014 Dihedral : 11.718 155.734 1644 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 22.32 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1382 helix: 0.95 (0.20), residues: 662 sheet: -0.88 (0.42), residues: 134 loop : -0.01 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 9 HIS 0.004 0.001 HIS A 304 PHE 0.019 0.002 PHE B 74 TYR 0.012 0.001 TYR A 498 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 517) hydrogen bonds : angle 5.11232 ( 1497) SS BOND : bond 0.00192 ( 2) SS BOND : angle 2.82750 ( 4) covalent geometry : bond 0.00431 (11748) covalent geometry : angle 0.54432 (15868) *********************** 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 178 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7225 (mp0) REVERT: A 144 MET cc_start: 0.8733 (mtm) cc_final: 0.8532 (mtm) REVERT: A 316 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 328 ASP cc_start: 0.7878 (m-30) cc_final: 0.7588 (m-30) REVERT: A 335 GLU cc_start: 0.7453 (pt0) cc_final: 0.7090 (pt0) REVERT: A 453 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8366 (ttt-90) REVERT: A 545 ASN cc_start: 0.8653 (m-40) cc_final: 0.8295 (m-40) REVERT: A 603 GLU cc_start: 0.7193 (tt0) cc_final: 0.6604 (tt0) REVERT: A 640 MET cc_start: 0.9067 (tpp) cc_final: 0.8820 (tpp) REVERT: A 658 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 660 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: B 11 GLN cc_start: 0.6863 (tt0) cc_final: 0.6520 (tt0) REVERT: B 43 GLN cc_start: 0.7738 (mt0) cc_final: 0.7482 (mt0) REVERT: B 131 ASN cc_start: 0.8139 (t0) cc_final: 0.7791 (t0) REVERT: B 240 MET cc_start: 0.3621 (OUTLIER) cc_final: 0.3003 (ppp) REVERT: B 384 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: B 393 SER cc_start: 0.8853 (t) cc_final: 0.8581 (t) REVERT: B 658 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 662 MET cc_start: 0.8021 (ptp) cc_final: 0.7150 (ptp) outliers start: 28 outliers final: 16 residues processed: 167 average time/residue: 1.2832 time to fit residues: 232.9477 Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 367 VAL 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 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 = 0.3703 r_free = 0.3703 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125286 restraints weight = 11435.523| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.40 r_work: 0.3241 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11750 Z= 0.145 Angle : 0.516 6.832 15872 Z= 0.268 Chirality : 0.041 0.156 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.499 152.013 1644 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.19 % Allowed : 22.32 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1382 helix: 1.08 (0.20), residues: 662 sheet: -0.89 (0.42), residues: 134 loop : -0.00 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.002 PHE B 74 TYR 0.011 0.001 TYR B 574 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 517) hydrogen bonds : angle 4.99580 ( 1497) SS BOND : bond 0.00210 ( 2) SS BOND : angle 2.53102 ( 4) covalent geometry : bond 0.00334 (11748) covalent geometry : angle 0.51471 (15868) *********************** 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 177 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.250 Fit side-chains REVERT: A 75 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7279 (mp0) REVERT: A 144 MET cc_start: 0.8702 (mtm) cc_final: 0.8485 (mtm) REVERT: A 316 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: A 328 ASP cc_start: 0.7731 (m-30) cc_final: 0.7431 (m-30) REVERT: A 335 GLU cc_start: 0.7440 (pt0) cc_final: 0.7109 (pt0) REVERT: A 545 ASN cc_start: 0.8624 (m-40) cc_final: 0.8287 (m-40) REVERT: A 632 MET cc_start: 0.9008 (mtt) cc_final: 0.8243 (mtt) REVERT: A 640 MET cc_start: 0.9077 (tpp) cc_final: 0.8825 (tpp) REVERT: A 658 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 11 GLN cc_start: 0.6737 (tt0) cc_final: 0.6103 (mt0) REVERT: B 43 GLN cc_start: 0.7728 (mt0) cc_final: 0.7468 (mt0) REVERT: B 240 MET cc_start: 0.3623 (OUTLIER) cc_final: 0.2994 (ppp) REVERT: B 384 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7952 (pp20) REVERT: B 393 SER cc_start: 0.8823 (t) cc_final: 0.8575 (t) REVERT: B 421 GLU cc_start: 0.8201 (pt0) cc_final: 0.7846 (pp20) REVERT: B 658 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7707 (mt) outliers start: 27 outliers final: 14 residues processed: 167 average time/residue: 1.2019 time to fit residues: 218.4790 Evaluate side-chains 166 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 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 62 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3637 r_free = 0.3637 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118894 restraints weight = 11574.136| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.40 r_work: 0.3150 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1755 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= 0.316 Angle : 0.646 8.697 15872 Z= 0.334 Chirality : 0.047 0.153 1686 Planarity : 0.004 0.042 2014 Dihedral : 12.213 167.887 1644 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.76 % Allowed : 21.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1382 helix: 0.61 (0.20), residues: 658 sheet: -0.98 (0.42), residues: 134 loop : -0.14 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.008 0.001 HIS B 568 PHE 0.027 0.002 PHE B 74 TYR 0.017 0.002 TYR B 85 ARG 0.005 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 517) hydrogen bonds : angle 5.44859 ( 1497) SS BOND : bond 0.00105 ( 2) SS BOND : angle 3.46327 ( 4) covalent geometry : bond 0.00748 (11748) covalent geometry : angle 0.64340 (15868) *********************** 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 185 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7735 (t70) cc_final: 0.7534 (t70) REVERT: A 316 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 328 ASP cc_start: 0.7962 (m-30) cc_final: 0.7712 (m-30) REVERT: A 335 GLU cc_start: 0.7585 (pt0) cc_final: 0.7194 (pt0) REVERT: A 453 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8386 (ttt-90) REVERT: A 545 ASN cc_start: 0.8603 (m-40) cc_final: 0.8215 (m-40) REVERT: A 603 GLU cc_start: 0.7414 (tt0) cc_final: 0.6846 (tt0) REVERT: A 658 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 660 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: B 11 GLN cc_start: 0.6890 (tt0) cc_final: 0.6440 (tm-30) REVERT: B 43 GLN cc_start: 0.7781 (mt0) cc_final: 0.7547 (mt0) REVERT: B 111 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7531 (mmtm) REVERT: B 240 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.2973 (ppp) REVERT: B 309 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: B 384 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8107 (pp20) REVERT: B 393 SER cc_start: 0.8910 (t) cc_final: 0.8638 (t) REVERT: B 658 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 662 MET cc_start: 0.8086 (ptp) cc_final: 0.7260 (ptp) outliers start: 34 outliers final: 18 residues processed: 171 average time/residue: 1.2984 time to fit residues: 240.2842 Evaluate side-chains 169 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 218 ASN 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 660 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.3702 r_free = 0.3702 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125456 restraints weight = 11391.018| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.40 r_work: 0.3229 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.139 Angle : 0.529 6.544 15872 Z= 0.275 Chirality : 0.041 0.157 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.559 156.419 1644 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.54 % Allowed : 23.13 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1382 helix: 0.94 (0.20), residues: 652 sheet: -0.98 (0.43), residues: 134 loop : -0.12 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.006 0.001 HIS B 568 PHE 0.021 0.002 PHE B 74 TYR 0.013 0.001 TYR B 574 ARG 0.009 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 517) hydrogen bonds : angle 5.06591 ( 1497) SS BOND : bond 0.00185 ( 2) SS BOND : angle 2.64848 ( 4) covalent geometry : bond 0.00322 (11748) covalent geometry : angle 0.52692 (15868) ********************** 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 170 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7285 (mp0) REVERT: A 328 ASP cc_start: 0.7819 (m-30) cc_final: 0.7575 (m-30) REVERT: A 545 ASN cc_start: 0.8618 (m-40) cc_final: 0.8281 (m-40) REVERT: A 603 GLU cc_start: 0.7236 (tt0) cc_final: 0.6578 (tt0) REVERT: A 632 MET cc_start: 0.9004 (mtt) cc_final: 0.8224 (mtt) REVERT: A 640 MET cc_start: 0.9077 (tpp) cc_final: 0.8846 (tpp) REVERT: A 658 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 11 GLN cc_start: 0.6701 (tt0) cc_final: 0.6322 (tm-30) REVERT: B 43 GLN cc_start: 0.7760 (mt0) cc_final: 0.7516 (mt0) REVERT: B 240 MET cc_start: 0.3626 (OUTLIER) cc_final: 0.3106 (ppp) REVERT: B 321 GLU cc_start: 0.8244 (tt0) cc_final: 0.8000 (tt0) REVERT: B 384 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7906 (pp20) REVERT: B 393 SER cc_start: 0.8823 (t) cc_final: 0.8570 (t) REVERT: B 421 GLU cc_start: 0.8152 (pt0) cc_final: 0.7826 (pp20) REVERT: B 658 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7692 (mt) outliers start: 19 outliers final: 14 residues processed: 162 average time/residue: 1.1580 time to fit residues: 204.5925 Evaluate side-chains 164 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 348 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 39 optimal weight: 0.0050 chunk 80 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117652 restraints weight = 12050.789| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.63 r_work: 0.3192 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1618 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= 0.133 Angle : 0.521 6.465 15872 Z= 0.270 Chirality : 0.041 0.156 1686 Planarity : 0.003 0.039 2014 Dihedral : 11.197 154.579 1644 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.79 % Allowed : 22.97 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1382 helix: 1.08 (0.20), residues: 650 sheet: -1.08 (0.42), residues: 134 loop : -0.10 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 9 HIS 0.006 0.001 HIS B 568 PHE 0.024 0.002 PHE B 98 TYR 0.012 0.001 TYR B 85 ARG 0.006 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 517) hydrogen bonds : angle 4.94929 ( 1497) SS BOND : bond 0.00203 ( 2) SS BOND : angle 2.59761 ( 4) covalent geometry : bond 0.00306 (11748) covalent geometry : angle 0.51903 (15868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8733.94 seconds wall clock time: 154 minutes 4.03 seconds (9244.03 seconds total)