Starting phenix.real_space_refine on Mon Apr 6 15:55:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.map" model { file = "/net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nnc_49571/04_2026/9nnc_49571.cif" } resolution = 2.4 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= -0.001 sd= 0.058 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 6514 2.51 5 N 1653 2.21 5 O 1735 1.98 5 H 9535 0.53 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 9726 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 36, 'TRANS': 604} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 9709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 9709 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 36, 'TRANS': 603} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.10, per 1000 atoms: 0.16 Number of scatterers: 19451 At special positions: 0 Unit cell: (123.654, 94.1735, 111.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 1735 8.00 N 1653 7.00 C 6514 6.00 H 9535 1.00 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: 1.51 Conformation dependent library (CDL) restraints added in 509.6 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 68.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 50 through 56 removed outlier: 4.404A pdb=" N GLN A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 89 removed outlier: 3.555A pdb=" N VAL A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.978A pdb=" N GLY A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 Processing helix chain 'A' and resid 140 through 143 removed outlier: 4.526A pdb=" N TRP A 143 " --> pdb=" O GLY A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.682A pdb=" N VAL A 172 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 201 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.955A pdb=" N LEU A 206 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.583A pdb=" N SER A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 227 through 228 No H-bonds generated for 'chain 'A' and resid 227 through 228' Processing helix chain 'A' and resid 229 through 254 removed outlier: 4.627A pdb=" N THR A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.544A pdb=" N HIS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.752A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 467 through 488 Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.589A pdb=" N SER A 680 " --> pdb=" O PRO A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 763 removed outlier: 3.575A pdb=" N ARG A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.723A pdb=" N LYS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 4.327A pdb=" N GLN B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 89 removed outlier: 3.635A pdb=" N LEU B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 93 through 111 removed outlier: 3.601A pdb=" N LEU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N CYS B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 139 Processing helix chain 'B' and resid 140 through 143 removed outlier: 4.349A pdb=" N TRP B 143 " --> pdb=" O GLY B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.574A pdb=" N VAL B 172 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 174 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 175 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 Proline residue: B 197 - end of helix Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 229 through 254 removed outlier: 4.420A pdb=" N THR B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 326 through 350 removed outlier: 3.653A pdb=" N HIS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 370 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.702A pdb=" N VAL B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.680A pdb=" N LEU B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 488 Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 617 through 636 Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.541A pdb=" N ARG B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 680 Processing helix chain 'B' and resid 747 through 763 removed outlier: 3.639A pdb=" N THR B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 514 removed outlier: 4.698A pdb=" N ILE A 537 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE A 536 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 609 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE A 538 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N HIS A 745 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 643 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 493 through 494 removed outlier: 6.148A pdb=" N PHE B 536 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP B 609 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE B 538 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 499 600 hydrogen bonds defined for protein. 1740 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: 4.35 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9529 1.03 - 1.23: 20 1.23 - 1.42: 4233 1.42 - 1.62: 5896 1.62 - 1.81: 22 Bond restraints: 19700 Sorted by residual: bond pdb=" NZ LYS B 308 " pdb=" HZ1 LYS B 308 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 308 " pdb=" HZ2 LYS B 308 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 288 " pdb=" HZ1 LYS B 288 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" NZ LYS A 288 " pdb=" HZ1 LYS A 288 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" NZ LYS B 288 " pdb=" HZ2 LYS B 288 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 19695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 34764 1.93 - 3.87: 558 3.87 - 5.80: 75 5.80 - 7.74: 18 7.74 - 9.67: 2 Bond angle restraints: 35417 Sorted by residual: angle pdb=" C SER B 508 " pdb=" CA SER B 508 " pdb=" CB SER B 508 " ideal model delta sigma weight residual 110.10 117.39 -7.29 1.90e+00 2.77e-01 1.47e+01 angle pdb=" N ARG B 509 " pdb=" CA ARG B 509 " pdb=" C ARG B 509 " ideal model delta sigma weight residual 110.14 105.03 5.11 1.47e+00 4.63e-01 1.21e+01 angle pdb=" C ASP B 510 " pdb=" CA ASP B 510 " pdb=" CB ASP B 510 " ideal model delta sigma weight residual 110.30 103.45 6.85 1.98e+00 2.55e-01 1.20e+01 angle pdb=" O VAL A 500 " pdb=" C VAL A 500 " pdb=" N HIS A 501 " ideal model delta sigma weight residual 123.18 119.46 3.72 1.08e+00 8.57e-01 1.19e+01 angle pdb=" C ASP A 510 " pdb=" CA ASP A 510 " pdb=" CB ASP A 510 " ideal model delta sigma weight residual 109.79 102.79 7.00 2.05e+00 2.38e-01 1.16e+01 ... (remaining 35412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8105 17.83 - 35.65: 874 35.65 - 53.48: 263 53.48 - 71.30: 93 71.30 - 89.13: 12 Dihedral angle restraints: 9347 sinusoidal: 4923 harmonic: 4424 Sorted by residual: dihedral pdb=" CA SER B 508 " pdb=" C SER B 508 " pdb=" N ARG B 509 " pdb=" CA ARG B 509 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA TYR A 375 " pdb=" C TYR A 375 " pdb=" N PRO A 376 " pdb=" CA PRO A 376 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" C ASP B 510 " pdb=" N ASP B 510 " pdb=" CA ASP B 510 " pdb=" CB ASP B 510 " ideal model delta harmonic sigma weight residual -122.60 -113.50 -9.10 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 9344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1245 0.048 - 0.095: 307 0.095 - 0.143: 65 0.143 - 0.190: 4 0.190 - 0.238: 2 Chirality restraints: 1623 Sorted by residual: chirality pdb=" CA SER B 543 " pdb=" N SER B 543 " pdb=" C SER B 543 " pdb=" CB SER B 543 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASP B 510 " pdb=" N ASP B 510 " pdb=" C ASP B 510 " pdb=" CB ASP B 510 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA ASP A 510 " pdb=" N ASP A 510 " pdb=" C ASP A 510 " pdb=" CB ASP A 510 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 1620 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 508 " -0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" N ARG B 509 " 0.066 2.00e-02 2.50e+03 pdb=" CA ARG B 509 " -0.018 2.00e-02 2.50e+03 pdb=" H ARG B 509 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 543 " -0.014 2.00e-02 2.50e+03 2.50e-02 6.24e+00 pdb=" N PHE B 544 " 0.043 2.00e-02 2.50e+03 pdb=" CA PHE B 544 " -0.011 2.00e-02 2.50e+03 pdb=" H PHE B 544 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 500 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL A 500 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 500 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS A 501 " 0.014 2.00e-02 2.50e+03 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 126 2.05 - 2.69: 29795 2.69 - 3.33: 58364 3.33 - 3.96: 75303 3.96 - 4.60: 117389 Nonbonded interactions: 280977 Sorted by model distance: nonbonded pdb="HG22 THR B 394 " pdb=" HD2 PRO B 395 " model vdw 1.413 2.440 nonbonded pdb=" HE3 LYS A 499 " pdb=" HB2 SER A 508 " model vdw 1.447 2.440 nonbonded pdb="HD11 LEU A 206 " pdb="HG22 THR A 208 " model vdw 1.533 2.440 nonbonded pdb="HG22 THR A 394 " pdb=" HD2 PRO A 395 " model vdw 1.543 2.440 nonbonded pdb=" HE2 TYR B 98 " pdb=" HD2 HIS B 309 " model vdw 1.569 2.100 ... (remaining 280972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 500 or resid 508 through 801)) selection = chain 'B' } 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: 7.620 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: 0.080 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.800 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10165 Z= 0.181 Angle : 0.705 9.670 13855 Z= 0.355 Chirality : 0.043 0.238 1623 Planarity : 0.006 0.061 1726 Dihedral : 14.889 89.126 3553 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.09 % Allowed : 15.70 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1257 helix: -0.09 (0.17), residues: 771 sheet: -0.15 (0.67), residues: 59 loop : -0.91 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.035 0.002 TYR B 134 PHE 0.031 0.002 PHE B 544 TRP 0.019 0.002 TRP B 55 HIS 0.007 0.002 HIS B 745 Details of bonding type rmsd covalent geometry : bond 0.00425 (10165) covalent geometry : angle 0.70541 (13855) hydrogen bonds : bond 0.24276 ( 600) hydrogen bonds : angle 7.53253 ( 1740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7212 (mp10) cc_final: 0.6699 (mt0) REVERT: A 321 LYS cc_start: 0.8075 (tttt) cc_final: 0.7459 (tmtt) REVERT: A 481 VAL cc_start: 0.8379 (m) cc_final: 0.8145 (t) REVERT: A 544 PHE cc_start: 0.3918 (OUTLIER) cc_final: 0.2848 (t80) REVERT: A 578 ARG cc_start: 0.6356 (ttp-110) cc_final: 0.5170 (ppt170) REVERT: A 650 TRP cc_start: 0.5820 (m100) cc_final: 0.5192 (m100) REVERT: B 54 GLN cc_start: 0.7082 (mp10) cc_final: 0.6510 (mt0) REVERT: B 173 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6993 (mt-10) REVERT: B 321 LYS cc_start: 0.7901 (tttt) cc_final: 0.7385 (tmtt) REVERT: B 566 ARG cc_start: 0.5202 (mtp85) cc_final: 0.4887 (tpt170) REVERT: B 640 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6174 (mp0) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.9792 time to fit residues: 102.5391 Evaluate side-chains 89 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 222 ASN A 642 HIS A 679 GLN B 309 HIS B 312 GLN B 326 HIS B 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143888 restraints weight = 31535.599| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.74 r_work: 0.3632 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10165 Z= 0.139 Angle : 0.545 6.470 13855 Z= 0.291 Chirality : 0.041 0.139 1623 Planarity : 0.006 0.057 1726 Dihedral : 4.994 66.221 1375 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.32 % Allowed : 14.85 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1257 helix: 1.31 (0.18), residues: 780 sheet: -0.30 (0.67), residues: 59 loop : -0.96 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.013 0.001 TYR A 375 PHE 0.034 0.002 PHE A 183 TRP 0.007 0.001 TRP B 281 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00294 (10165) covalent geometry : angle 0.54486 (13855) hydrogen bonds : bond 0.05983 ( 600) hydrogen bonds : angle 4.81108 ( 1740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7180 (mp10) cc_final: 0.6640 (mt0) REVERT: A 321 LYS cc_start: 0.8043 (tttt) cc_final: 0.7331 (tmtt) REVERT: A 544 PHE cc_start: 0.4002 (OUTLIER) cc_final: 0.2857 (t80) REVERT: A 578 ARG cc_start: 0.6473 (ttp-110) cc_final: 0.4959 (ppt170) REVERT: A 650 TRP cc_start: 0.5746 (m100) cc_final: 0.5075 (m100) REVERT: B 54 GLN cc_start: 0.7110 (mp10) cc_final: 0.6510 (mt0) REVERT: B 216 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (mp) REVERT: B 321 LYS cc_start: 0.7841 (tttt) cc_final: 0.7263 (tmtt) REVERT: B 566 ARG cc_start: 0.5131 (mtp85) cc_final: 0.4709 (tpt170) REVERT: B 650 TRP cc_start: 0.5650 (m100) cc_final: 0.5122 (m100) outliers start: 14 outliers final: 6 residues processed: 115 average time/residue: 0.9740 time to fit residues: 122.2377 Evaluate side-chains 103 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 79 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 204 ASN B 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141893 restraints weight = 31701.496| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.76 r_work: 0.3609 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10165 Z= 0.146 Angle : 0.535 6.467 13855 Z= 0.281 Chirality : 0.041 0.202 1623 Planarity : 0.005 0.054 1726 Dihedral : 4.627 55.207 1375 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 1.70 % Allowed : 15.52 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1257 helix: 1.76 (0.18), residues: 775 sheet: -0.23 (0.69), residues: 60 loop : -1.15 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 539 TYR 0.016 0.001 TYR A 375 PHE 0.032 0.002 PHE B 183 TRP 0.010 0.001 TRP A 446 HIS 0.006 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00331 (10165) covalent geometry : angle 0.53514 (13855) hydrogen bonds : bond 0.05349 ( 600) hydrogen bonds : angle 4.45462 ( 1740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.526 Fit side-chains REVERT: A 54 GLN cc_start: 0.7215 (mp10) cc_final: 0.6603 (mt0) REVERT: A 321 LYS cc_start: 0.8039 (tttt) cc_final: 0.7351 (tmtt) REVERT: A 544 PHE cc_start: 0.4094 (OUTLIER) cc_final: 0.2782 (t80) REVERT: A 578 ARG cc_start: 0.6648 (ttp-110) cc_final: 0.5131 (ppt170) REVERT: A 628 ARG cc_start: 0.6953 (ttp-170) cc_final: 0.6655 (ttp-110) REVERT: A 650 TRP cc_start: 0.5840 (m100) cc_final: 0.5172 (m100) REVERT: B 54 GLN cc_start: 0.7155 (mp10) cc_final: 0.6585 (mt0) REVERT: B 216 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 220 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (mm) REVERT: B 253 ARG cc_start: 0.7295 (mmm-85) cc_final: 0.6987 (ttt180) REVERT: B 321 LYS cc_start: 0.7758 (tttt) cc_final: 0.7201 (tmtt) REVERT: B 566 ARG cc_start: 0.5351 (mtp85) cc_final: 0.4894 (tpt170) REVERT: B 650 TRP cc_start: 0.5848 (m100) cc_final: 0.5246 (m100) outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 0.8692 time to fit residues: 118.7312 Evaluate side-chains 106 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 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 222 ASN A 326 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140477 restraints weight = 31710.144| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.75 r_work: 0.3591 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10165 Z= 0.158 Angle : 0.539 7.620 13855 Z= 0.282 Chirality : 0.041 0.141 1623 Planarity : 0.006 0.057 1726 Dihedral : 4.630 55.459 1375 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.93 % Favored : 94.83 % Rotamer: Outliers : 1.42 % Allowed : 16.37 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1257 helix: 1.80 (0.18), residues: 782 sheet: -0.01 (0.70), residues: 59 loop : -1.24 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.016 0.001 TYR A 375 PHE 0.028 0.002 PHE B 183 TRP 0.006 0.001 TRP B 170 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00363 (10165) covalent geometry : angle 0.53911 (13855) hydrogen bonds : bond 0.05268 ( 600) hydrogen bonds : angle 4.40491 ( 1740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.477 Fit side-chains REVERT: A 54 GLN cc_start: 0.7266 (mp10) cc_final: 0.6660 (mt0) REVERT: A 321 LYS cc_start: 0.8054 (tttt) cc_final: 0.7362 (tmtt) REVERT: A 544 PHE cc_start: 0.3995 (OUTLIER) cc_final: 0.2627 (t80) REVERT: A 578 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5217 (ppt170) REVERT: A 628 ARG cc_start: 0.6978 (ttp-170) cc_final: 0.6754 (ttp-170) REVERT: A 650 TRP cc_start: 0.5852 (m100) cc_final: 0.5213 (m100) REVERT: B 54 GLN cc_start: 0.7216 (mp10) cc_final: 0.6599 (mt0) REVERT: B 216 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 254 TYR cc_start: 0.7206 (m-80) cc_final: 0.6972 (m-10) REVERT: B 321 LYS cc_start: 0.7750 (tttt) cc_final: 0.7129 (tmtt) REVERT: B 566 ARG cc_start: 0.5539 (mtp85) cc_final: 0.4988 (tpt170) REVERT: B 650 TRP cc_start: 0.5836 (m100) cc_final: 0.5247 (m100) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.8254 time to fit residues: 113.8942 Evaluate side-chains 116 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 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 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141450 restraints weight = 31843.669| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.74 r_work: 0.3608 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10165 Z= 0.142 Angle : 0.523 7.341 13855 Z= 0.273 Chirality : 0.041 0.131 1623 Planarity : 0.005 0.051 1726 Dihedral : 4.504 55.070 1375 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Rotamer: Outliers : 1.89 % Allowed : 16.18 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1257 helix: 1.92 (0.18), residues: 784 sheet: -0.02 (0.72), residues: 59 loop : -1.17 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 753 TYR 0.014 0.001 TYR A 375 PHE 0.026 0.002 PHE B 183 TRP 0.005 0.001 TRP B 170 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00324 (10165) covalent geometry : angle 0.52341 (13855) hydrogen bonds : bond 0.04982 ( 600) hydrogen bonds : angle 4.31253 ( 1740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7277 (mp10) cc_final: 0.6682 (mt0) REVERT: A 321 LYS cc_start: 0.8115 (tttt) cc_final: 0.7437 (tmtt) REVERT: A 544 PHE cc_start: 0.3953 (OUTLIER) cc_final: 0.2604 (t80) REVERT: A 578 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5312 (ppt170) REVERT: A 628 ARG cc_start: 0.6945 (ttp-170) cc_final: 0.6643 (ttp-110) REVERT: A 650 TRP cc_start: 0.5827 (m100) cc_final: 0.5208 (m100) REVERT: B 54 GLN cc_start: 0.7224 (mp10) cc_final: 0.6618 (mt0) REVERT: B 216 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 321 LYS cc_start: 0.7819 (tttt) cc_final: 0.7188 (tmtt) REVERT: B 566 ARG cc_start: 0.5612 (mtp85) cc_final: 0.5040 (tpt170) REVERT: B 640 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6350 (mp0) REVERT: B 650 TRP cc_start: 0.5920 (m100) cc_final: 0.5311 (m100) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.8286 time to fit residues: 113.6159 Evaluate side-chains 121 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 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 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140749 restraints weight = 31603.874| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.74 r_work: 0.3599 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10165 Z= 0.153 Angle : 0.531 6.912 13855 Z= 0.278 Chirality : 0.041 0.138 1623 Planarity : 0.005 0.054 1726 Dihedral : 4.499 54.767 1375 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Rotamer: Outliers : 1.99 % Allowed : 16.65 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1257 helix: 1.92 (0.18), residues: 784 sheet: -0.04 (0.72), residues: 59 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.016 0.001 TYR A 375 PHE 0.026 0.002 PHE A 183 TRP 0.006 0.001 TRP A 170 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00354 (10165) covalent geometry : angle 0.53059 (13855) hydrogen bonds : bond 0.05078 ( 600) hydrogen bonds : angle 4.31263 ( 1740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7293 (mp10) cc_final: 0.6656 (mt0) REVERT: A 321 LYS cc_start: 0.8106 (tttt) cc_final: 0.7428 (tmtt) REVERT: A 544 PHE cc_start: 0.3944 (OUTLIER) cc_final: 0.2573 (t80) REVERT: A 578 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5354 (ppt170) REVERT: A 628 ARG cc_start: 0.6976 (ttp-170) cc_final: 0.6660 (ttp-110) REVERT: A 650 TRP cc_start: 0.5877 (m100) cc_final: 0.5262 (m100) REVERT: B 54 GLN cc_start: 0.7225 (mp10) cc_final: 0.6625 (mt0) REVERT: B 216 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 321 LYS cc_start: 0.7824 (tttt) cc_final: 0.7192 (tmtt) REVERT: B 566 ARG cc_start: 0.5677 (mtp85) cc_final: 0.5112 (tpt170) REVERT: B 640 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6336 (mp0) REVERT: B 650 TRP cc_start: 0.5937 (m100) cc_final: 0.5334 (m100) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.8807 time to fit residues: 122.4215 Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139782 restraints weight = 31779.133| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.75 r_work: 0.3582 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10165 Z= 0.150 Angle : 0.537 7.728 13855 Z= 0.279 Chirality : 0.041 0.136 1623 Planarity : 0.005 0.053 1726 Dihedral : 4.474 54.523 1375 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.93 % Favored : 94.83 % Rotamer: Outliers : 1.80 % Allowed : 17.22 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1257 helix: 1.97 (0.19), residues: 784 sheet: -0.12 (0.71), residues: 59 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.015 0.001 TYR B 134 PHE 0.030 0.002 PHE B 183 TRP 0.006 0.001 TRP A 170 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00345 (10165) covalent geometry : angle 0.53721 (13855) hydrogen bonds : bond 0.05018 ( 600) hydrogen bonds : angle 4.29887 ( 1740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.546 Fit side-chains REVERT: A 54 GLN cc_start: 0.7290 (mp10) cc_final: 0.6649 (mt0) REVERT: A 321 LYS cc_start: 0.8080 (tttt) cc_final: 0.7379 (tmtt) REVERT: A 544 PHE cc_start: 0.3956 (OUTLIER) cc_final: 0.2507 (t80) REVERT: A 578 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5124 (ptt-90) REVERT: A 628 ARG cc_start: 0.6966 (ttp-170) cc_final: 0.6653 (ttp-110) REVERT: A 650 TRP cc_start: 0.5873 (m100) cc_final: 0.5263 (m100) REVERT: B 54 GLN cc_start: 0.7236 (mp10) cc_final: 0.6622 (mt0) REVERT: B 216 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 321 LYS cc_start: 0.7879 (tttt) cc_final: 0.7218 (tmtt) REVERT: B 566 ARG cc_start: 0.5753 (mtp85) cc_final: 0.5151 (tpt170) REVERT: B 640 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6386 (mp0) REVERT: B 650 TRP cc_start: 0.5976 (m100) cc_final: 0.5359 (m100) outliers start: 19 outliers final: 12 residues processed: 121 average time/residue: 0.9029 time to fit residues: 120.7107 Evaluate side-chains 120 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140032 restraints weight = 31565.698| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.76 r_work: 0.3587 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10165 Z= 0.145 Angle : 0.539 9.252 13855 Z= 0.280 Chirality : 0.041 0.137 1623 Planarity : 0.005 0.051 1726 Dihedral : 4.446 54.266 1375 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Rotamer: Outliers : 1.99 % Allowed : 17.41 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.24), residues: 1257 helix: 1.99 (0.19), residues: 784 sheet: -0.12 (0.71), residues: 59 loop : -1.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.015 0.001 TYR A 375 PHE 0.029 0.002 PHE B 183 TRP 0.006 0.001 TRP A 170 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00332 (10165) covalent geometry : angle 0.53913 (13855) hydrogen bonds : bond 0.04920 ( 600) hydrogen bonds : angle 4.28848 ( 1740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7273 (mp10) cc_final: 0.6637 (mt0) REVERT: A 321 LYS cc_start: 0.8079 (tttt) cc_final: 0.7370 (tmtt) REVERT: A 544 PHE cc_start: 0.3982 (OUTLIER) cc_final: 0.2496 (t80) REVERT: A 578 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5123 (ptt-90) REVERT: A 628 ARG cc_start: 0.6951 (ttp-170) cc_final: 0.6638 (ttp-110) REVERT: A 650 TRP cc_start: 0.5874 (m100) cc_final: 0.5265 (m100) REVERT: B 54 GLN cc_start: 0.7228 (mp10) cc_final: 0.6618 (mt0) REVERT: B 216 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 253 ARG cc_start: 0.7233 (ttm170) cc_final: 0.7022 (ttt180) REVERT: B 321 LYS cc_start: 0.7864 (tttt) cc_final: 0.7314 (tmtt) REVERT: B 566 ARG cc_start: 0.5764 (mtp85) cc_final: 0.5183 (tpt170) REVERT: B 640 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6383 (mp0) REVERT: B 650 TRP cc_start: 0.6002 (m100) cc_final: 0.5392 (m100) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.9183 time to fit residues: 123.0967 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 559 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140573 restraints weight = 31443.367| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.74 r_work: 0.3595 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10165 Z= 0.133 Angle : 0.525 7.774 13855 Z= 0.272 Chirality : 0.041 0.143 1623 Planarity : 0.005 0.050 1726 Dihedral : 4.377 53.987 1375 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.77 % Favored : 94.99 % Rotamer: Outliers : 1.51 % Allowed : 17.69 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1257 helix: 2.05 (0.19), residues: 784 sheet: -0.13 (0.71), residues: 59 loop : -1.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 566 TYR 0.014 0.001 TYR A 134 PHE 0.028 0.002 PHE B 183 TRP 0.005 0.001 TRP A 170 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00301 (10165) covalent geometry : angle 0.52503 (13855) hydrogen bonds : bond 0.04719 ( 600) hydrogen bonds : angle 4.24456 ( 1740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.459 Fit side-chains REVERT: A 54 GLN cc_start: 0.7265 (mp10) cc_final: 0.6629 (mt0) REVERT: A 321 LYS cc_start: 0.8091 (tttt) cc_final: 0.7358 (tmtt) REVERT: A 544 PHE cc_start: 0.3940 (OUTLIER) cc_final: 0.2445 (t80) REVERT: A 578 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5310 (ppt170) REVERT: A 628 ARG cc_start: 0.6925 (ttp-170) cc_final: 0.6623 (ttp-110) REVERT: A 650 TRP cc_start: 0.5851 (m100) cc_final: 0.5242 (m100) REVERT: B 54 GLN cc_start: 0.7221 (mp10) cc_final: 0.6614 (mt0) REVERT: B 216 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 253 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6990 (ttt180) REVERT: B 321 LYS cc_start: 0.7865 (tttt) cc_final: 0.7204 (tmtt) REVERT: B 566 ARG cc_start: 0.5783 (mtp85) cc_final: 0.5171 (tpt170) REVERT: B 640 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6402 (mp0) REVERT: B 650 TRP cc_start: 0.5989 (m100) cc_final: 0.5401 (m100) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.8937 time to fit residues: 114.1301 Evaluate side-chains 116 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.164998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139677 restraints weight = 31834.271| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.75 r_work: 0.3583 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10165 Z= 0.149 Angle : 0.537 7.524 13855 Z= 0.280 Chirality : 0.041 0.142 1623 Planarity : 0.005 0.052 1726 Dihedral : 4.416 53.947 1375 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.93 % Favored : 94.83 % Rotamer: Outliers : 1.61 % Allowed : 17.60 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.24), residues: 1257 helix: 2.01 (0.18), residues: 784 sheet: -0.12 (0.71), residues: 59 loop : -1.27 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.016 0.001 TYR A 375 PHE 0.030 0.002 PHE B 183 TRP 0.006 0.001 TRP A 55 HIS 0.008 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00344 (10165) covalent geometry : angle 0.53720 (13855) hydrogen bonds : bond 0.04942 ( 600) hydrogen bonds : angle 4.28185 ( 1740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.490 Fit side-chains REVERT: A 54 GLN cc_start: 0.7272 (mp10) cc_final: 0.6637 (mt0) REVERT: A 321 LYS cc_start: 0.8098 (tttt) cc_final: 0.7385 (tmtt) REVERT: A 544 PHE cc_start: 0.3924 (OUTLIER) cc_final: 0.2439 (t80) REVERT: A 578 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5124 (ptt-90) REVERT: A 628 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6638 (ttp-110) REVERT: A 650 TRP cc_start: 0.5873 (m100) cc_final: 0.5266 (m100) REVERT: B 54 GLN cc_start: 0.7267 (mp10) cc_final: 0.6660 (mt0) REVERT: B 216 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 321 LYS cc_start: 0.7885 (tttt) cc_final: 0.7228 (tmtt) REVERT: B 566 ARG cc_start: 0.5860 (mtp85) cc_final: 0.5208 (tpt170) REVERT: B 640 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6386 (mp0) REVERT: B 650 TRP cc_start: 0.5994 (m100) cc_final: 0.5396 (m100) outliers start: 17 outliers final: 12 residues processed: 114 average time/residue: 0.8935 time to fit residues: 111.6820 Evaluate side-chains 115 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.164732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139409 restraints weight = 31714.048| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.76 r_work: 0.3578 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10165 Z= 0.159 Angle : 0.551 7.438 13855 Z= 0.287 Chirality : 0.042 0.147 1623 Planarity : 0.005 0.055 1726 Dihedral : 4.478 54.168 1375 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.09 % Favored : 94.67 % Rotamer: Outliers : 1.70 % Allowed : 17.50 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1257 helix: 1.96 (0.18), residues: 784 sheet: -0.18 (0.70), residues: 59 loop : -1.30 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.016 0.001 TYR A 375 PHE 0.031 0.002 PHE B 183 TRP 0.006 0.001 TRP A 55 HIS 0.009 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00368 (10165) covalent geometry : angle 0.55131 (13855) hydrogen bonds : bond 0.05087 ( 600) hydrogen bonds : angle 4.31973 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6449.83 seconds wall clock time: 109 minutes 53.80 seconds (6593.80 seconds total)