Starting phenix.real_space_refine on Wed May 14 05:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.map" model { file = "/net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byh_45031/05_2025/9byh_45031.cif" } resolution = 2.53 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= 0.002 sd= 0.129 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 7302 2.51 5 N 1904 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11524 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: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 119 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 119 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} 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: 7.64, per 1000 atoms: 0.66 Number of scatterers: 11524 At special positions: 0 Unit cell: (91.53, 71.19, 132.21, 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 2240 8.00 N 1904 7.00 C 7302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 53.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.096A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.987A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.961A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.674A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 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 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.065A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.580A 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 removed outlier: 3.666A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.398A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.848A 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 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 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 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.622A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.115A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.052A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.961A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.678A 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: 3.897A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.866A 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 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.648A 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 removed outlier: 3.712A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.008A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.129A 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 442 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 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.072A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) 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 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.366A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.484A 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: 6.613A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.488A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.178A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.067A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 515 hydrogen bonds defined for protein. 1509 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: 3.52 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3690 1.34 - 1.46: 2772 1.46 - 1.58: 5176 1.58 - 1.70: 26 1.70 - 1.81: 112 Bond restraints: 11776 Sorted by residual: bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CA ASP A 398 " pdb=" CB ASP A 398 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.06e+00 bond pdb=" C5 GDP B 804 " pdb=" C4 GDP B 804 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CB MET A 493 " pdb=" CG MET A 493 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.49e-01 bond pdb=" C5 GDP A 802 " pdb=" C4 GDP A 802 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.22e-01 ... (remaining 11771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15734 1.92 - 3.85: 150 3.85 - 5.77: 15 5.77 - 7.69: 3 7.69 - 9.62: 2 Bond angle restraints: 15904 Sorted by residual: angle pdb=" CB MET A 493 " pdb=" CG MET A 493 " pdb=" SD MET A 493 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C TYR A 397 " pdb=" N ASP A 398 " pdb=" CA ASP A 398 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" CB MET A 595 " pdb=" CG MET A 595 " pdb=" SD MET A 595 " ideal model delta sigma weight residual 112.70 121.39 -8.69 3.00e+00 1.11e-01 8.38e+00 angle pdb=" CA MET A 493 " pdb=" CB MET A 493 " pdb=" CG MET A 493 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" N ASP D 318 " pdb=" CA ASP D 318 " pdb=" C ASP D 318 " ideal model delta sigma weight residual 113.72 110.18 3.54 1.52e+00 4.33e-01 5.42e+00 ... (remaining 15899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6801 35.69 - 71.39: 280 71.39 - 107.08: 27 107.08 - 142.78: 3 142.78 - 178.47: 3 Dihedral angle restraints: 7114 sinusoidal: 2978 harmonic: 4136 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.15 -178.47 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.02 150.66 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.03 148.94 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 7111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1004 0.028 - 0.055: 440 0.055 - 0.083: 152 0.083 - 0.110: 74 0.110 - 0.138: 20 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA ILE A 652 " pdb=" N ILE A 652 " pdb=" C ILE A 652 " pdb=" CB ILE A 652 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-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 4.74e-01 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 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1687 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 35 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C SER B 35 " -0.023 2.00e-02 2.50e+03 pdb=" O SER B 35 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 36 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 100 " -0.011 2.00e-02 2.50e+03 8.51e-03 1.27e+00 pdb=" CG PHE B 100 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 100 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 100 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 100 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 100 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 100 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 579 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO A 580 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " 0.015 5.00e-02 4.00e+02 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 168 2.62 - 3.19: 10149 3.19 - 3.76: 20484 3.76 - 4.33: 29686 4.33 - 4.90: 46484 Nonbonded interactions: 106971 Sorted by model distance: nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 2.047 2.170 nonbonded pdb=" O2A TTP A 803 " pdb="MG MG A 804 " model vdw 2.077 2.170 nonbonded pdb=" O PRO A 616 " pdb=" OH TYR A 626 " model vdw 2.128 3.040 nonbonded pdb=" O PRO B 616 " pdb=" OH TYR B 626 " model vdw 2.137 3.040 nonbonded pdb=" O3G TTP B 801 " pdb="MG MG B 802 " model vdw 2.175 2.170 ... (remaining 106966 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } 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: 0.720 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.370 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.002 0.034 11776 Z= 0.111 Angle : 0.497 9.616 15904 Z= 0.260 Chirality : 0.039 0.138 1690 Planarity : 0.003 0.027 2018 Dihedral : 18.813 178.470 4454 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.89 % Allowed : 19.53 % Favored : 79.58 % 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: 0.89 (0.22), residues: 1386 helix: 1.01 (0.20), residues: 678 sheet: 0.40 (0.41), residues: 124 loop : 0.32 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.002 0.000 HIS B 255 PHE 0.019 0.001 PHE B 100 TYR 0.017 0.001 TYR A 612 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.13019 ( 513) hydrogen bonds : angle 6.54373 ( 1509) covalent geometry : bond 0.00242 (11776) covalent geometry : angle 0.49658 (15904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 321 TYR cc_start: 0.8864 (m-80) cc_final: 0.8567 (m-80) outliers start: 11 outliers final: 10 residues processed: 177 average time/residue: 1.2156 time to fit residues: 233.1786 Evaluate side-chains 170 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 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 = 0.3573 r_free = 0.3573 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111734 restraints weight = 10657.993| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.42 r_work: 0.3065 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11776 Z= 0.200 Angle : 0.560 7.230 15904 Z= 0.296 Chirality : 0.043 0.147 1690 Planarity : 0.003 0.032 2018 Dihedral : 13.362 174.237 1665 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.16 % Allowed : 16.53 % Favored : 80.31 % 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: 0.96 (0.22), residues: 1386 helix: 1.12 (0.20), residues: 668 sheet: -0.03 (0.42), residues: 126 loop : 0.40 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.005 0.001 HIS A 438 PHE 0.021 0.002 PHE B 100 TYR 0.016 0.002 TYR A 612 ARG 0.003 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 513) hydrogen bonds : angle 5.34327 ( 1509) covalent geometry : bond 0.00457 (11776) covalent geometry : angle 0.56005 (15904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.310 Fit side-chains REVERT: A 33 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7346 (p) REVERT: A 384 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8466 (pp20) REVERT: A 402 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 518 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7609 (mp0) REVERT: B 19 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: B 214 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6943 (mtmm) REVERT: B 665 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7620 (tmt170) REVERT: C 321 TYR cc_start: 0.8330 (m-80) cc_final: 0.8091 (m-80) outliers start: 39 outliers final: 14 residues processed: 190 average time/residue: 1.2810 time to fit residues: 263.1918 Evaluate side-chains 181 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 665 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 113 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 232 ASN ** B 338 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 = 0.3608 r_free = 0.3608 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115158 restraints weight = 10897.080| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.44 r_work: 0.3115 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11776 Z= 0.129 Angle : 0.498 6.534 15904 Z= 0.263 Chirality : 0.041 0.138 1690 Planarity : 0.003 0.026 2018 Dihedral : 12.814 176.339 1654 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % 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: 1.07 (0.22), residues: 1386 helix: 1.33 (0.20), residues: 658 sheet: -0.08 (0.42), residues: 126 loop : 0.35 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 9 HIS 0.005 0.001 HIS A 438 PHE 0.020 0.002 PHE B 100 TYR 0.013 0.001 TYR A 612 ARG 0.002 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 513) hydrogen bonds : angle 5.03459 ( 1509) covalent geometry : bond 0.00288 (11776) covalent geometry : angle 0.49847 (15904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.248 Fit side-chains REVERT: A 33 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7338 (p) REVERT: A 42 ASN cc_start: 0.8630 (m-40) cc_final: 0.8414 (m-40) REVERT: A 52 LYS cc_start: 0.7454 (tmtt) cc_final: 0.7189 (tmtt) REVERT: A 384 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8456 (pp20) REVERT: A 402 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 423 LYS cc_start: 0.8434 (mttm) cc_final: 0.8192 (mtpt) REVERT: A 483 GLU cc_start: 0.8279 (mp0) cc_final: 0.8059 (mp0) REVERT: A 518 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7570 (mp0) REVERT: B 19 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: B 304 HIS cc_start: 0.8599 (t70) cc_final: 0.8165 (t70) REVERT: B 530 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (pttm) REVERT: C 321 TYR cc_start: 0.8290 (m-80) cc_final: 0.7887 (m-80) outliers start: 29 outliers final: 13 residues processed: 191 average time/residue: 1.2654 time to fit residues: 261.1361 Evaluate side-chains 182 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 338 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 = 0.3548 r_free = 0.3548 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109201 restraints weight = 10800.499| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.43 r_work: 0.3039 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11776 Z= 0.267 Angle : 0.608 7.460 15904 Z= 0.321 Chirality : 0.046 0.181 1690 Planarity : 0.004 0.034 2018 Dihedral : 13.160 171.019 1652 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.32 % Allowed : 17.83 % Favored : 78.85 % 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: 0.69 (0.22), residues: 1386 helix: 0.93 (0.20), residues: 668 sheet: -0.29 (0.42), residues: 126 loop : 0.26 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.024 0.003 PHE B 100 TYR 0.017 0.002 TYR B 498 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 513) hydrogen bonds : angle 5.34675 ( 1509) covalent geometry : bond 0.00616 (11776) covalent geometry : angle 0.60782 (15904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.227 Fit side-chains REVERT: A 33 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7526 (p) REVERT: A 384 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8531 (pp20) REVERT: A 423 LYS cc_start: 0.8538 (mttm) cc_final: 0.8262 (mtpt) REVERT: A 518 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7686 (mp0) REVERT: B 15 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: B 19 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: B 43 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: B 384 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: C 316 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6833 (mtpt) outliers start: 41 outliers final: 21 residues processed: 188 average time/residue: 1.3182 time to fit residues: 267.1752 Evaluate side-chains 187 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.142518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112510 restraints weight = 10881.136| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.44 r_work: 0.3082 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11776 Z= 0.162 Angle : 0.530 7.445 15904 Z= 0.280 Chirality : 0.042 0.148 1690 Planarity : 0.003 0.034 2018 Dihedral : 12.796 174.167 1652 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.84 % Allowed : 18.80 % Favored : 78.36 % 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: 0.77 (0.22), residues: 1386 helix: 1.08 (0.20), residues: 668 sheet: -0.56 (0.48), residues: 98 loop : 0.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.022 0.002 PHE B 100 TYR 0.016 0.001 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 513) hydrogen bonds : angle 5.11152 ( 1509) covalent geometry : bond 0.00368 (11776) covalent geometry : angle 0.53005 (15904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.289 Fit side-chains REVERT: A 33 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 42 ASN cc_start: 0.8654 (m-40) cc_final: 0.8434 (m-40) REVERT: A 362 ASP cc_start: 0.8651 (m-30) cc_final: 0.8447 (m-30) REVERT: A 384 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8455 (pp20) REVERT: A 423 LYS cc_start: 0.8518 (mttm) cc_final: 0.8259 (mtpt) REVERT: A 518 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7619 (mp0) REVERT: B 15 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 43 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 384 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8237 (pp20) REVERT: B 658 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 321 TYR cc_start: 0.8296 (m-80) cc_final: 0.8071 (m-80) outliers start: 35 outliers final: 16 residues processed: 188 average time/residue: 1.2663 time to fit residues: 257.5064 Evaluate side-chains 185 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 17 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112178 restraints weight = 10940.687| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.44 r_work: 0.3078 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11776 Z= 0.168 Angle : 0.536 6.619 15904 Z= 0.282 Chirality : 0.042 0.144 1690 Planarity : 0.003 0.037 2018 Dihedral : 12.712 174.418 1652 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 19.45 % Favored : 78.12 % 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: 0.84 (0.22), residues: 1386 helix: 1.10 (0.20), residues: 668 sheet: -0.25 (0.43), residues: 126 loop : 0.28 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 PHE 0.021 0.002 PHE B 100 TYR 0.016 0.001 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 513) hydrogen bonds : angle 5.10112 ( 1509) covalent geometry : bond 0.00383 (11776) covalent geometry : angle 0.53637 (15904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.352 Fit side-chains REVERT: A 33 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (p) REVERT: A 42 ASN cc_start: 0.8655 (m-40) cc_final: 0.8423 (m-40) REVERT: A 362 ASP cc_start: 0.8665 (m-30) cc_final: 0.8457 (m-30) REVERT: A 384 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: A 423 LYS cc_start: 0.8539 (mttm) cc_final: 0.8260 (mtpt) REVERT: A 518 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7603 (mp0) REVERT: A 662 MET cc_start: 0.8444 (ptp) cc_final: 0.8149 (ptm) REVERT: B 15 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: B 19 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 43 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: B 274 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6933 (ttm-80) REVERT: B 384 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: B 658 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8021 (mt) outliers start: 30 outliers final: 17 residues processed: 191 average time/residue: 1.2391 time to fit residues: 255.9908 Evaluate side-chains 190 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 133 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 89 optimal weight: 0.0170 chunk 118 optimal weight: 3.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113229 restraints weight = 10972.271| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.45 r_work: 0.3090 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11776 Z= 0.148 Angle : 0.523 8.286 15904 Z= 0.274 Chirality : 0.041 0.141 1690 Planarity : 0.003 0.038 2018 Dihedral : 12.538 175.976 1652 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.35 % Allowed : 19.94 % Favored : 77.71 % 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: 1386 helix: 1.15 (0.20), residues: 672 sheet: -0.57 (0.49), residues: 98 loop : 0.26 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.021 0.002 PHE B 100 TYR 0.018 0.001 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 513) hydrogen bonds : angle 5.02685 ( 1509) covalent geometry : bond 0.00335 (11776) covalent geometry : angle 0.52266 (15904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.239 Fit side-chains REVERT: A 33 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 235 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7656 (mtt180) REVERT: A 362 ASP cc_start: 0.8674 (m-30) cc_final: 0.8442 (m-30) REVERT: A 384 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: A 402 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 423 LYS cc_start: 0.8476 (mttm) cc_final: 0.8208 (mtpt) REVERT: A 518 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7589 (mp0) REVERT: B 15 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: B 43 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: B 240 MET cc_start: 0.5143 (mpt) cc_final: 0.4893 (mpt) REVERT: B 274 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6937 (ttm-80) REVERT: B 384 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: B 658 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8018 (mt) REVERT: C 321 TYR cc_start: 0.8241 (m-80) cc_final: 0.7884 (m-80) outliers start: 29 outliers final: 17 residues processed: 191 average time/residue: 1.3156 time to fit residues: 271.1649 Evaluate side-chains 187 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 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 = 0.3574 r_free = 0.3574 target = 0.141912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111642 restraints weight = 10910.455| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.44 r_work: 0.3066 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11776 Z= 0.187 Angle : 0.558 8.697 15904 Z= 0.293 Chirality : 0.043 0.146 1690 Planarity : 0.003 0.039 2018 Dihedral : 12.622 174.171 1652 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.67 % Allowed : 19.85 % Favored : 77.47 % 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: 0.80 (0.22), residues: 1386 helix: 1.06 (0.20), residues: 670 sheet: -0.28 (0.43), residues: 126 loop : 0.28 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.021 0.002 PHE B 100 TYR 0.018 0.002 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 513) hydrogen bonds : angle 5.12429 ( 1509) covalent geometry : bond 0.00429 (11776) covalent geometry : angle 0.55782 (15904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.325 Fit side-chains REVERT: A 33 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7459 (p) REVERT: A 362 ASP cc_start: 0.8683 (m-30) cc_final: 0.8468 (m-30) REVERT: A 384 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: A 402 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7006 (tm-30) REVERT: A 423 LYS cc_start: 0.8527 (mttm) cc_final: 0.8263 (mtpt) REVERT: A 518 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7648 (mp0) REVERT: A 662 MET cc_start: 0.8341 (ptm) cc_final: 0.8135 (ptm) REVERT: B 15 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: B 19 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: B 43 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: B 274 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7006 (ttm-80) REVERT: B 384 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: C 316 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6921 (mtpt) outliers start: 33 outliers final: 17 residues processed: 188 average time/residue: 1.3399 time to fit residues: 271.2273 Evaluate side-chains 185 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113847 restraints weight = 10942.461| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.45 r_work: 0.3101 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11776 Z= 0.143 Angle : 0.529 9.031 15904 Z= 0.277 Chirality : 0.041 0.141 1690 Planarity : 0.003 0.039 2018 Dihedral : 12.396 176.197 1652 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.94 % Allowed : 20.75 % Favored : 77.31 % 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: 0.87 (0.22), residues: 1386 helix: 1.17 (0.20), residues: 672 sheet: -0.57 (0.49), residues: 98 loop : 0.26 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.021 0.002 PHE B 100 TYR 0.021 0.001 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 513) hydrogen bonds : angle 5.00713 ( 1509) covalent geometry : bond 0.00326 (11776) covalent geometry : angle 0.52941 (15904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.218 Fit side-chains REVERT: A 33 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7478 (p) REVERT: A 235 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7623 (mtt180) REVERT: A 362 ASP cc_start: 0.8674 (m-30) cc_final: 0.8455 (m-30) REVERT: A 384 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8480 (pp20) REVERT: A 402 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 423 LYS cc_start: 0.8451 (mttm) cc_final: 0.8212 (mtpt) REVERT: A 518 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7574 (mp0) REVERT: B 15 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: B 43 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 274 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6922 (ttm-80) REVERT: B 384 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8293 (pp20) REVERT: C 321 TYR cc_start: 0.8155 (m-80) cc_final: 0.7928 (m-80) outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 1.3087 time to fit residues: 264.0642 Evaluate side-chains 192 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.110857 restraints weight = 10875.543| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.44 r_work: 0.3056 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11776 Z= 0.214 Angle : 0.586 9.216 15904 Z= 0.307 Chirality : 0.044 0.149 1690 Planarity : 0.003 0.041 2018 Dihedral : 12.609 173.203 1652 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.03 % Allowed : 20.91 % Favored : 77.07 % 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: 0.66 (0.22), residues: 1386 helix: 0.98 (0.20), residues: 670 sheet: -0.67 (0.49), residues: 98 loop : 0.19 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 PHE 0.022 0.002 PHE B 100 TYR 0.025 0.002 TYR A 612 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 513) hydrogen bonds : angle 5.18339 ( 1509) covalent geometry : bond 0.00492 (11776) covalent geometry : angle 0.58634 (15904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.226 Fit side-chains REVERT: A 33 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7508 (p) REVERT: A 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.8476 (m-30) REVERT: A 384 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8512 (pp20) REVERT: A 402 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 423 LYS cc_start: 0.8518 (mttm) cc_final: 0.8244 (mtpt) REVERT: A 518 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7629 (mp0) REVERT: B 15 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: B 19 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: B 43 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: B 384 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: C 316 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6962 (mtpt) outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 1.2945 time to fit residues: 251.4563 Evaluate side-chains 183 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115600 restraints weight = 10894.764| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.44 r_work: 0.3126 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11776 Z= 0.123 Angle : 0.519 9.771 15904 Z= 0.270 Chirality : 0.041 0.141 1690 Planarity : 0.003 0.038 2018 Dihedral : 12.197 178.011 1652 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.94 % Allowed : 20.99 % Favored : 77.07 % 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: 0.87 (0.22), residues: 1386 helix: 1.22 (0.20), residues: 674 sheet: -0.80 (0.48), residues: 102 loop : 0.24 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.021 0.002 PHE B 100 TYR 0.020 0.001 TYR A 612 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 513) hydrogen bonds : angle 4.94247 ( 1509) covalent geometry : bond 0.00279 (11776) covalent geometry : angle 0.51897 (15904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8467.23 seconds wall clock time: 147 minutes 7.66 seconds (8827.66 seconds total)