Starting phenix.real_space_refine on Wed Sep 17 21:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byh_45031/09_2025/9byh_45031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byh_45031/09_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_45031/09_2025/9byh_45031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byh_45031/09_2025/9byh_45031.map" model { file = "/net/cci-nas-00/data/ceres_data/9byh_45031/09_2025/9byh_45031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byh_45031/09_2025/9byh_45031.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.92, per 1000 atoms: 0.25 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: 0.99 Conformation dependent library (CDL) restraints added in 537.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.27 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: 1.62 Time building geometry restraints manager: 1.33 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: 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: 0.02 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (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 ARG 0.002 0.000 ARG A 243 TYR 0.017 0.001 TYR A 612 PHE 0.019 0.001 PHE B 100 TRP 0.007 0.001 TRP B 9 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00242 (11776) covalent geometry : angle 0.49658 (15904) hydrogen bonds : bond 0.13019 ( 513) hydrogen bonds : angle 6.54373 ( 1509) *********************** 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 : 0.468 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: 0.6355 time to fit residues: 121.4639 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 : 0.458 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 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 44 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 338 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 = 0.3540 r_free = 0.3540 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108977 restraints weight = 10965.766| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.41 r_work: 0.3036 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11776 Z= 0.267 Angle : 0.611 7.621 15904 Z= 0.323 Chirality : 0.046 0.180 1690 Planarity : 0.004 0.035 2018 Dihedral : 13.593 172.480 1665 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.24 % Allowed : 16.29 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.22), residues: 1386 helix: 0.94 (0.20), residues: 668 sheet: -0.09 (0.42), residues: 126 loop : 0.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 207 TYR 0.018 0.002 TYR A 612 PHE 0.025 0.002 PHE B 100 TRP 0.007 0.002 TRP A 558 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00615 (11776) covalent geometry : angle 0.61056 (15904) hydrogen bonds : bond 0.04730 ( 513) hydrogen bonds : angle 5.50064 ( 1509) *********************** 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 201 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.491 Fit side-chains REVERT: A 33 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 384 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: A 398 ASP cc_start: 0.6843 (p0) cc_final: 0.6642 (p0) REVERT: A 402 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 518 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7648 (mp0) REVERT: B 19 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: B 665 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7642 (tmt170) REVERT: C 316 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7208 (mttt) outliers start: 40 outliers final: 15 residues processed: 186 average time/residue: 0.6392 time to fit residues: 127.9286 Evaluate side-chains 177 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 621 ASN 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 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 410 ASN Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.144579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114816 restraints weight = 10969.810| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.44 r_work: 0.3109 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0945 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= 0.126 Angle : 0.498 6.592 15904 Z= 0.263 Chirality : 0.041 0.138 1690 Planarity : 0.003 0.026 2018 Dihedral : 12.926 176.807 1656 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.59 % Allowed : 17.67 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.22), residues: 1386 helix: 1.29 (0.20), residues: 656 sheet: -0.45 (0.47), residues: 98 loop : 0.24 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.013 0.001 TYR A 612 PHE 0.020 0.002 PHE B 100 TRP 0.007 0.002 TRP B 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00280 (11776) covalent geometry : angle 0.49786 (15904) hydrogen bonds : bond 0.03620 ( 513) hydrogen bonds : angle 5.05789 ( 1509) *********************** 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 201 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.395 Fit side-chains REVERT: A 33 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7353 (p) REVERT: A 110 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6267 (p0) REVERT: A 235 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7743 (mtt90) REVERT: A 384 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8426 (pp20) REVERT: A 402 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 423 LYS cc_start: 0.8420 (mttm) cc_final: 0.8188 (mtpt) REVERT: A 483 GLU cc_start: 0.8260 (mp0) cc_final: 0.8047 (mp0) REVERT: A 518 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7569 (mp0) REVERT: A 551 HIS cc_start: 0.8513 (t70) cc_final: 0.8227 (t70) REVERT: B 19 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: B 304 HIS cc_start: 0.8614 (t70) cc_final: 0.8176 (t70) REVERT: C 316 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6900 (mtpt) REVERT: C 321 TYR cc_start: 0.8267 (m-80) cc_final: 0.7921 (m-80) outliers start: 32 outliers final: 14 residues processed: 191 average time/residue: 0.6327 time to fit residues: 130.3583 Evaluate side-chains 184 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 554 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 0.0030 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115733 restraints weight = 10958.826| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.45 r_work: 0.3121 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11776 Z= 0.121 Angle : 0.488 6.245 15904 Z= 0.256 Chirality : 0.040 0.137 1690 Planarity : 0.003 0.030 2018 Dihedral : 12.532 177.495 1654 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.08 % Allowed : 17.99 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1386 helix: 1.31 (0.20), residues: 672 sheet: -0.12 (0.43), residues: 126 loop : 0.39 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 235 TYR 0.012 0.001 TYR A 612 PHE 0.019 0.001 PHE B 100 TRP 0.006 0.001 TRP A 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00269 (11776) covalent geometry : angle 0.48786 (15904) hydrogen bonds : bond 0.03443 ( 513) hydrogen bonds : angle 4.93041 ( 1509) *********************** 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 215 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.486 Fit side-chains REVERT: A 33 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7402 (p) REVERT: A 110 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6264 (p0) REVERT: A 235 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7720 (mtt90) REVERT: A 384 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8417 (pp20) REVERT: A 402 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 423 LYS cc_start: 0.8444 (mttm) cc_final: 0.8206 (mtpt) REVERT: A 483 GLU cc_start: 0.8270 (mp0) cc_final: 0.8037 (mp0) REVERT: A 518 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7555 (mp0) REVERT: A 551 HIS cc_start: 0.8486 (t70) cc_final: 0.8225 (t70) REVERT: B 15 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: B 19 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: B 304 HIS cc_start: 0.8556 (t70) cc_final: 0.8132 (t70) REVERT: B 384 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: B 658 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 316 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6904 (mtpt) REVERT: C 321 TYR cc_start: 0.8272 (m-80) cc_final: 0.7869 (m-80) outliers start: 38 outliers final: 14 residues processed: 200 average time/residue: 0.6380 time to fit residues: 137.3260 Evaluate side-chains 194 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 658 LEU 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 64 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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 = 0.3578 r_free = 0.3578 target = 0.142237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112049 restraints weight = 10924.050| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.44 r_work: 0.3077 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1164 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= 0.183 Angle : 0.543 7.583 15904 Z= 0.286 Chirality : 0.043 0.148 1690 Planarity : 0.003 0.034 2018 Dihedral : 12.733 174.155 1654 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.51 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.22), residues: 1386 helix: 1.13 (0.20), residues: 670 sheet: -0.22 (0.43), residues: 126 loop : 0.31 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.014 0.001 TYR A 612 PHE 0.021 0.002 PHE A 100 TRP 0.007 0.002 TRP A 9 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00416 (11776) covalent geometry : angle 0.54266 (15904) hydrogen bonds : bond 0.03931 ( 513) hydrogen bonds : angle 5.10236 ( 1509) *********************** 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 198 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7406 (p) REVERT: A 110 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6282 (p0) REVERT: A 384 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: A 423 LYS cc_start: 0.8486 (mttm) cc_final: 0.8228 (mtpt) REVERT: A 518 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7636 (mp0) REVERT: A 567 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 15 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: B 19 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: B 384 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: B 658 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 316 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6936 (mtpt) outliers start: 31 outliers final: 16 residues processed: 188 average time/residue: 0.6422 time to fit residues: 130.0961 Evaluate side-chains 186 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 567 GLU 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 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 421 GLU 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 658 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 86 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.144022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114009 restraints weight = 10900.088| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.44 r_work: 0.3102 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1168 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= 0.145 Angle : 0.516 7.955 15904 Z= 0.270 Chirality : 0.041 0.142 1690 Planarity : 0.003 0.035 2018 Dihedral : 12.548 175.941 1654 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.84 % Allowed : 19.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.22), residues: 1386 helix: 1.19 (0.20), residues: 672 sheet: -0.61 (0.48), residues: 98 loop : 0.27 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.015 0.001 TYR A 612 PHE 0.020 0.002 PHE B 100 TRP 0.006 0.002 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00327 (11776) covalent geometry : angle 0.51592 (15904) hydrogen bonds : bond 0.03620 ( 513) hydrogen bonds : angle 4.99109 ( 1509) *********************** 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: 35 poor density : 166 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7391 (p) REVERT: A 110 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6303 (p0) REVERT: A 384 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8478 (pp20) REVERT: A 402 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 423 LYS cc_start: 0.8482 (mttm) cc_final: 0.8243 (mtpt) REVERT: A 518 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7577 (mp0) REVERT: A 567 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 15 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: B 19 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: B 384 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8263 (pp20) REVERT: B 658 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7928 (mt) REVERT: C 316 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6962 (mtpt) REVERT: C 321 TYR cc_start: 0.8227 (m-80) cc_final: 0.7894 (m-80) outliers start: 35 outliers final: 17 residues processed: 188 average time/residue: 0.6168 time to fit residues: 124.8836 Evaluate side-chains 190 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 567 GLU 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 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 421 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.3608 r_free = 0.3608 target = 0.144967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115015 restraints weight = 10834.859| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.44 r_work: 0.3111 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11776 Z= 0.132 Angle : 0.510 8.436 15904 Z= 0.266 Chirality : 0.041 0.140 1690 Planarity : 0.003 0.036 2018 Dihedral : 12.375 176.921 1654 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.35 % Allowed : 20.10 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.22), residues: 1386 helix: 1.24 (0.20), residues: 674 sheet: -0.42 (0.42), residues: 130 loop : 0.31 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.017 0.001 TYR A 612 PHE 0.019 0.002 PHE B 100 TRP 0.006 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00298 (11776) covalent geometry : angle 0.50971 (15904) hydrogen bonds : bond 0.03493 ( 513) hydrogen bonds : angle 4.93782 ( 1509) *********************** 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 203 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7380 (p) REVERT: A 110 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6297 (p0) REVERT: A 384 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8473 (pp20) REVERT: A 402 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7017 (tm-30) REVERT: A 423 LYS cc_start: 0.8484 (mttm) cc_final: 0.8216 (mtpt) REVERT: A 483 GLU cc_start: 0.8301 (mp0) cc_final: 0.8059 (mp0) REVERT: A 518 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7552 (mp0) REVERT: A 567 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 662 MET cc_start: 0.8406 (ptp) cc_final: 0.8163 (ptm) REVERT: B 15 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: B 19 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: B 274 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7007 (ttm-80) REVERT: B 304 HIS cc_start: 0.8649 (t70) cc_final: 0.8200 (t70) REVERT: B 384 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8268 (pp20) REVERT: B 658 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 321 TYR cc_start: 0.8205 (m-80) cc_final: 0.7844 (m-80) outliers start: 29 outliers final: 15 residues processed: 191 average time/residue: 0.6435 time to fit residues: 132.2824 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 : 0.481 ------------------------------------------------------------------------------- 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 567 GLU 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 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 570 MET Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 658 LEU 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 24 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 61 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 474 GLN B 232 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117603 restraints weight = 10912.093| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.45 r_work: 0.3150 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11776 Z= 0.111 Angle : 0.497 8.688 15904 Z= 0.257 Chirality : 0.040 0.135 1690 Planarity : 0.003 0.034 2018 Dihedral : 12.094 178.927 1654 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.35 % Allowed : 20.66 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.22), residues: 1386 helix: 1.38 (0.20), residues: 674 sheet: -0.40 (0.42), residues: 130 loop : 0.32 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.017 0.001 TYR A 612 PHE 0.018 0.001 PHE B 100 TRP 0.007 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00248 (11776) covalent geometry : angle 0.49667 (15904) hydrogen bonds : bond 0.03222 ( 513) hydrogen bonds : angle 4.82093 ( 1509) *********************** 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 211 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7374 (p) REVERT: A 110 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6331 (p0) REVERT: A 131 ASN cc_start: 0.8126 (t0) cc_final: 0.7652 (t0) REVERT: A 362 ASP cc_start: 0.8654 (m-30) cc_final: 0.8451 (m-30) REVERT: A 384 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: A 402 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6988 (tm-30) REVERT: A 423 LYS cc_start: 0.8498 (mttm) cc_final: 0.8227 (mtpt) REVERT: A 483 GLU cc_start: 0.8293 (mp0) cc_final: 0.8058 (mp0) REVERT: A 518 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7547 (mp0) REVERT: A 602 GLU cc_start: 0.8333 (pt0) cc_final: 0.7872 (pt0) REVERT: A 662 MET cc_start: 0.8358 (ptp) cc_final: 0.8101 (ptm) REVERT: B 15 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 19 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: B 304 HIS cc_start: 0.8488 (t70) cc_final: 0.8082 (t70) REVERT: B 384 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8118 (pp20) REVERT: B 658 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 316 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6986 (mtpt) REVERT: C 321 TYR cc_start: 0.8194 (m-80) cc_final: 0.7746 (m-80) outliers start: 29 outliers final: 13 residues processed: 198 average time/residue: 0.6276 time to fit residues: 134.0874 Evaluate side-chains 189 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 384 GLU 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 658 LEU 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 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** A 545 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117671 restraints weight = 10830.596| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.43 r_work: 0.3150 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1274 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= 0.115 Angle : 0.503 9.512 15904 Z= 0.260 Chirality : 0.040 0.136 1690 Planarity : 0.003 0.032 2018 Dihedral : 11.955 177.928 1654 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.11 % Allowed : 20.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.22), residues: 1386 helix: 1.37 (0.20), residues: 676 sheet: -0.48 (0.40), residues: 138 loop : 0.38 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.017 0.001 TYR A 612 PHE 0.018 0.001 PHE B 100 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00259 (11776) covalent geometry : angle 0.50268 (15904) hydrogen bonds : bond 0.03251 ( 513) hydrogen bonds : angle 4.79768 ( 1509) *********************** 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 201 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7363 (p) REVERT: A 110 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6229 (p0) REVERT: A 131 ASN cc_start: 0.8108 (t0) cc_final: 0.7639 (t0) REVERT: A 362 ASP cc_start: 0.8618 (m-30) cc_final: 0.8410 (m-30) REVERT: A 384 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8409 (pp20) REVERT: A 402 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 423 LYS cc_start: 0.8460 (mttm) cc_final: 0.8151 (mtpt) REVERT: A 483 GLU cc_start: 0.8215 (mp0) cc_final: 0.7969 (mp0) REVERT: A 518 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7543 (mp0) REVERT: A 662 MET cc_start: 0.8373 (ptp) cc_final: 0.8124 (ptm) REVERT: B 15 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: B 19 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: B 235 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7969 (mtm110) REVERT: B 304 HIS cc_start: 0.8422 (t70) cc_final: 0.8017 (t70) REVERT: B 384 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8142 (pp20) REVERT: B 658 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7875 (mt) REVERT: C 316 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7001 (mtpt) REVERT: C 321 TYR cc_start: 0.8183 (m-80) cc_final: 0.7724 (m-80) outliers start: 26 outliers final: 16 residues processed: 190 average time/residue: 0.6170 time to fit residues: 126.5065 Evaluate side-chains 196 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR 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 634 MET Chi-restraints excluded: chain B residue 658 LEU 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 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 19 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114146 restraints weight = 10917.529| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.45 r_work: 0.3105 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1270 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= 0.167 Angle : 0.543 9.974 15904 Z= 0.283 Chirality : 0.042 0.144 1690 Planarity : 0.003 0.036 2018 Dihedral : 12.105 175.387 1654 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.03 % Allowed : 21.31 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.22), residues: 1386 helix: 1.23 (0.20), residues: 672 sheet: -0.43 (0.42), residues: 130 loop : 0.29 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 235 TYR 0.022 0.001 TYR A 612 PHE 0.019 0.002 PHE B 487 TRP 0.008 0.002 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00381 (11776) covalent geometry : angle 0.54333 (15904) hydrogen bonds : bond 0.03651 ( 513) hydrogen bonds : angle 4.93081 ( 1509) ********************** 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 192 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7394 (p) REVERT: A 110 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6298 (p0) REVERT: A 131 ASN cc_start: 0.8238 (t0) cc_final: 0.7699 (t0) REVERT: A 384 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8499 (pp20) REVERT: A 423 LYS cc_start: 0.8496 (mttm) cc_final: 0.8228 (mttt) REVERT: A 483 GLU cc_start: 0.8296 (mp0) cc_final: 0.8082 (mp0) REVERT: A 518 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7582 (mp0) REVERT: A 602 GLU cc_start: 0.8485 (pt0) cc_final: 0.8058 (pt0) REVERT: A 662 MET cc_start: 0.8391 (ptp) cc_final: 0.8137 (ptm) REVERT: B 15 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: B 19 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: B 304 HIS cc_start: 0.8654 (t70) cc_final: 0.8215 (t70) REVERT: B 384 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: B 658 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 316 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7010 (mtpt) REVERT: C 321 TYR cc_start: 0.8197 (m-80) cc_final: 0.7856 (m-80) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.6324 time to fit residues: 125.4892 Evaluate side-chains 186 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR 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 634 MET Chi-restraints excluded: chain B residue 658 LEU 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 95 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A 545 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115779 restraints weight = 10919.383| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.45 r_work: 0.3129 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11776 Z= 0.132 Angle : 0.520 9.898 15904 Z= 0.270 Chirality : 0.041 0.140 1690 Planarity : 0.003 0.035 2018 Dihedral : 12.020 176.687 1654 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.19 % Allowed : 21.39 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.22), residues: 1386 helix: 1.28 (0.20), residues: 674 sheet: -0.50 (0.41), residues: 138 loop : 0.36 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 235 TYR 0.020 0.001 TYR A 612 PHE 0.018 0.002 PHE B 100 TRP 0.007 0.001 TRP A 9 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00300 (11776) covalent geometry : angle 0.52009 (15904) hydrogen bonds : bond 0.03436 ( 513) hydrogen bonds : angle 4.87152 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4371.02 seconds wall clock time: 75 minutes 33.91 seconds (4533.91 seconds total)