Starting phenix.real_space_refine on Wed Feb 4 17:51:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6v_47601/02_2026/9e6v_47601.map" } resolution = 3.5 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= 0.018 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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 P 2 5.49 5 S 43 5.16 5 C 8011 2.51 5 N 1931 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12128 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5967 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 690} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5975 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 691} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 102 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.21 Number of scatterers: 12128 At special positions: 0 Unit cell: (104.328, 110.952, 131.652, 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 43 16.00 P 2 15.00 O 2141 8.00 N 1931 7.00 C 8011 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 Links applied MAN-THR " MAN C 801 " - " THR C 13 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 440.5 milliseconds 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 55.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.722A pdb=" N TYR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 4.016A pdb=" N LYS B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 137 through 163 removed outlier: 3.916A pdb=" N VAL B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 166 through 179 removed outlier: 3.801A pdb=" N VAL B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.768A pdb=" N LEU B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 217 Processing helix chain 'B' and resid 220 through 241 Processing helix chain 'B' and resid 244 through 264 Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 286 through 304 removed outlier: 3.606A pdb=" N PHE B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.611A pdb=" N VAL B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 596 through 623 Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 638 through 652 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 666 through 685 removed outlier: 3.550A pdb=" N LEU B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 739 Proline residue: B 735 - end of helix Processing helix chain 'B' and resid 744 through 750 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.720A pdb=" N TYR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.974A pdb=" N LYS A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 137 through 163 removed outlier: 3.916A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.801A pdb=" N VAL A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.768A pdb=" N LEU A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 Processing helix chain 'A' and resid 220 through 241 Processing helix chain 'A' and resid 244 through 264 Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.603A pdb=" N PHE A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.509A pdb=" N ASP A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.663A pdb=" N VAL A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 558 Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 596 through 623 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 638 through 652 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 665 through 685 Processing helix chain 'A' and resid 711 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 744 through 750 Processing sheet with id=AA1, first strand: chain 'B' and resid 339 through 344 removed outlier: 13.271A pdb=" N ILE B 340 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N SER B 353 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE B 342 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 354 " --> pdb=" O GLN B 373 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN B 373 " --> pdb=" O HIS B 354 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 372 through 377 current: chain 'B' and resid 407 through 412 removed outlier: 13.287A pdb=" N ILE B 408 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N ALA B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 410 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 417 " --> pdb=" O HIS B 412 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 420 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 438 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N HIS B 422 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR B 436 " --> pdb=" O HIS B 422 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL B 424 " --> pdb=" O GLU B 434 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 433 through 439 current: chain 'B' and resid 473 through 478 removed outlier: 13.817A pdb=" N PHE B 474 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N THR B 487 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 476 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 579 through 584 removed outlier: 6.363A pdb=" N ILE B 591 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 583 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS B 589 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 344 removed outlier: 13.270A pdb=" N ILE A 340 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER A 353 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE A 342 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS A 354 " --> pdb=" O GLN A 373 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A 373 " --> pdb=" O HIS A 354 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 372 through 377 current: chain 'A' and resid 407 through 412 removed outlier: 13.284A pdb=" N ILE A 408 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 10.046A pdb=" N ALA A 421 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A 410 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 417 " --> pdb=" O HIS A 412 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 420 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 438 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS A 422 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR A 436 " --> pdb=" O HIS A 422 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL A 424 " --> pdb=" O GLU A 434 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 433 through 439 current: chain 'A' and resid 473 through 478 removed outlier: 13.816A pdb=" N PHE A 474 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 487 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU A 476 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 584 removed outlier: 6.362A pdb=" N ILE A 591 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 583 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 589 " --> pdb=" O THR A 583 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1626 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: 1.60 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1858 1.29 - 1.42: 3769 1.42 - 1.56: 6835 1.56 - 1.69: 7 1.69 - 1.82: 65 Bond restraints: 12534 Sorted by residual: bond pdb=" C HIS A 664 " pdb=" O HIS A 664 " ideal model delta sigma weight residual 1.236 1.401 -0.165 1.28e-02 6.10e+03 1.67e+02 bond pdb=" C LEU A 671 " pdb=" O LEU A 671 " ideal model delta sigma weight residual 1.236 1.332 -0.096 1.15e-02 7.56e+03 6.91e+01 bond pdb=" C LEU A 667 " pdb=" O LEU A 667 " ideal model delta sigma weight residual 1.238 1.319 -0.081 1.28e-02 6.10e+03 3.99e+01 bond pdb=" C TYR A 666 " pdb=" O TYR A 666 " ideal model delta sigma weight residual 1.236 1.156 0.079 1.29e-02 6.01e+03 3.78e+01 bond pdb=" C LEU A 663 " pdb=" O LEU A 663 " ideal model delta sigma weight residual 1.235 1.310 -0.074 1.26e-02 6.30e+03 3.47e+01 ... (remaining 12529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 15001 2.55 - 5.10: 1963 5.10 - 7.65: 89 7.65 - 10.20: 17 10.20 - 12.75: 7 Bond angle restraints: 17077 Sorted by residual: angle pdb=" O LYS A 323 " pdb=" C LYS A 323 " pdb=" N ASP A 324 " ideal model delta sigma weight residual 122.65 111.81 10.84 1.22e+00 6.72e-01 7.90e+01 angle pdb=" CA HIS A 664 " pdb=" C HIS A 664 " pdb=" O HIS A 664 " ideal model delta sigma weight residual 119.49 129.62 -10.13 1.21e+00 6.83e-01 7.02e+01 angle pdb=" N TYR A 666 " pdb=" CA TYR A 666 " pdb=" C TYR A 666 " ideal model delta sigma weight residual 112.54 102.38 10.16 1.22e+00 6.72e-01 6.94e+01 angle pdb=" C LYS A 323 " pdb=" N ASP A 324 " pdb=" CA ASP A 324 " ideal model delta sigma weight residual 121.42 132.67 -11.25 1.43e+00 4.89e-01 6.19e+01 angle pdb=" N TYR A 666 " pdb=" CA TYR A 666 " pdb=" CB TYR A 666 " ideal model delta sigma weight residual 110.39 123.14 -12.75 1.66e+00 3.63e-01 5.90e+01 ... (remaining 17072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 7078 34.31 - 68.62: 122 68.62 - 102.94: 8 102.94 - 137.25: 3 137.25 - 171.56: 1 Dihedral angle restraints: 7212 sinusoidal: 2866 harmonic: 4346 Sorted by residual: dihedral pdb=" C33 CPL A 801 " pdb=" C31 CPL A 801 " pdb=" C32 CPL A 801 " pdb=" O2 CPL A 801 " ideal model delta sinusoidal sigma weight residual 171.65 0.09 171.56 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PRO B 135 " pdb=" C PRO B 135 " pdb=" N ALA B 136 " pdb=" CA ALA B 136 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N CPL B 801 " pdb=" C4 CPL B 801 " pdb=" C5 CPL B 801 " pdb=" O4P CPL B 801 " ideal model delta sinusoidal sigma weight residual 288.92 164.37 124.55 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 7209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1067 0.068 - 0.135: 556 0.135 - 0.203: 169 0.203 - 0.271: 38 0.271 - 0.338: 7 Chirality restraints: 1837 Sorted by residual: chirality pdb=" CA ASN A 164 " pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CB ASN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA THR B 187 " pdb=" N THR B 187 " pdb=" C THR B 187 " pdb=" CB THR B 187 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASN B 164 " pdb=" N ASN B 164 " pdb=" C ASN B 164 " pdb=" CB ASN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1834 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 242 " -0.082 2.00e-02 2.50e+03 5.43e-02 5.90e+01 pdb=" CG TYR A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 242 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 242 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 242 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 242 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 242 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 242 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 242 " 0.081 2.00e-02 2.50e+03 5.42e-02 5.88e+01 pdb=" CG TYR B 242 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 242 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 242 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 242 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 242 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR B 242 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR B 242 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " -0.070 2.00e-02 2.50e+03 4.44e-02 4.92e+01 pdb=" CG TRP A 40 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " 0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " -0.064 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 97 2.62 - 3.19: 10581 3.19 - 3.76: 19824 3.76 - 4.33: 27993 4.33 - 4.90: 45628 Nonbonded interactions: 104123 Sorted by model distance: nonbonded pdb=" OD2 ASP A 80 " pdb=" O6 MAN C 801 " model vdw 2.046 3.040 nonbonded pdb=" OE1 GLU A 76 " pdb=" NE1 TRP A 582 " model vdw 2.170 3.120 nonbonded pdb=" O PHE A 754 " pdb=" N ILE A 756 " model vdw 2.171 3.120 nonbonded pdb=" O ILE B 367 " pdb=" N THR C 2 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 317 " pdb=" NZ LYS A 543 " model vdw 2.260 3.120 ... (remaining 104118 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 36 through 538 or (resid 539 and (name N or name CA or nam \ e C or name O or name CB )) or resid 540 through 762 or (resid 801 and (name C1 \ or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name \ C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or \ name C42 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 36 through 557 or (resid 558 and (name N or name CA or nam \ e C or name O or name CB )) or resid 559 through 762 or (resid 801 and (name C1 \ or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name \ C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or \ name C42 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.220 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.014 0.165 12535 Z= 0.790 Angle : 1.687 19.245 17079 Z= 1.137 Chirality : 0.087 0.338 1837 Planarity : 0.015 0.262 2125 Dihedral : 12.910 171.559 4410 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.91 % Favored : 94.61 % Rotamer: Outliers : 0.84 % Allowed : 1.15 % Favored : 98.01 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.74 % 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: -0.13 (0.20), residues: 1465 helix: 0.15 (0.18), residues: 718 sheet: -0.97 (0.53), residues: 83 loop : -0.04 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 409 TYR 0.100 0.016 TYR B 242 PHE 0.052 0.011 PHE A 455 TRP 0.081 0.016 TRP A 486 HIS 0.020 0.006 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.01348 (12534) covalent geometry : angle 1.67888 (17077) hydrogen bonds : bond 0.15562 ( 577) hydrogen bonds : angle 6.63110 ( 1626) link_MAN-THR : bond 0.13630 ( 1) link_MAN-THR : angle 15.27109 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 80 ASP cc_start: 0.8418 (m-30) cc_final: 0.8130 (m-30) REVERT: A 104 PHE cc_start: 0.8887 (t80) cc_final: 0.8579 (t80) REVERT: A 126 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 539 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 553 PHE cc_start: 0.8691 (m-80) cc_final: 0.8443 (m-10) REVERT: A 718 PHE cc_start: 0.8857 (t80) cc_final: 0.8584 (t80) outliers start: 11 outliers final: 4 residues processed: 214 average time/residue: 0.0899 time to fit residues: 28.8249 Evaluate side-chains 108 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 HIS A 354 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.147729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111676 restraints weight = 19170.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110995 restraints weight = 11755.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111709 restraints weight = 10764.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112515 restraints weight = 6997.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112899 restraints weight = 6209.917| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12535 Z= 0.151 Angle : 0.563 7.724 17079 Z= 0.296 Chirality : 0.044 0.157 1837 Planarity : 0.004 0.064 2125 Dihedral : 9.064 162.567 1682 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 5.05 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.18 (0.21), residues: 1465 helix: 1.66 (0.19), residues: 718 sheet: -0.87 (0.52), residues: 97 loop : 0.15 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.034 0.002 TYR A 118 PHE 0.015 0.001 PHE B 318 TRP 0.018 0.001 TRP A 681 HIS 0.008 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00314 (12534) covalent geometry : angle 0.56255 (17077) hydrogen bonds : bond 0.05508 ( 577) hydrogen bonds : angle 4.53663 ( 1626) link_MAN-THR : bond 0.01993 ( 1) link_MAN-THR : angle 2.40423 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.7960 (mmm) cc_final: 0.7627 (mtp) REVERT: A 108 MET cc_start: 0.8036 (mmm) cc_final: 0.7818 (tpt) REVERT: A 126 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 543 LYS cc_start: 0.9005 (tppt) cc_final: 0.8801 (mptt) REVERT: A 631 MET cc_start: 0.8440 (mmp) cc_final: 0.8215 (tpp) REVERT: A 729 PHE cc_start: 0.9007 (t80) cc_final: 0.8636 (t80) REVERT: C 15 SER cc_start: 0.8454 (p) cc_final: 0.8171 (t) outliers start: 17 outliers final: 8 residues processed: 132 average time/residue: 0.0933 time to fit residues: 18.7372 Evaluate side-chains 98 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN ** B 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN A 354 HIS A 563 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.141956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106491 restraints weight = 19654.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105233 restraints weight = 12660.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105398 restraints weight = 14560.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107203 restraints weight = 7687.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107693 restraints weight = 5926.215| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12535 Z= 0.174 Angle : 0.537 6.677 17079 Z= 0.281 Chirality : 0.044 0.174 1837 Planarity : 0.004 0.053 2125 Dihedral : 8.306 137.071 1678 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.00 % Allowed : 6.05 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.22), residues: 1465 helix: 1.69 (0.19), residues: 717 sheet: -1.29 (0.48), residues: 110 loop : 0.13 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.023 0.001 TYR A 118 PHE 0.021 0.002 PHE A 642 TRP 0.019 0.001 TRP B 223 HIS 0.021 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00421 (12534) covalent geometry : angle 0.53723 (17077) hydrogen bonds : bond 0.05307 ( 577) hydrogen bonds : angle 4.42878 ( 1626) link_MAN-THR : bond 0.01510 ( 1) link_MAN-THR : angle 1.14153 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.304 Fit side-chains REVERT: B 108 MET cc_start: 0.8029 (mmm) cc_final: 0.7647 (mtp) REVERT: B 467 LEU cc_start: 0.9020 (tp) cc_final: 0.8798 (tt) REVERT: A 80 ASP cc_start: 0.7554 (m-30) cc_final: 0.7282 (m-30) REVERT: A 108 MET cc_start: 0.8125 (mmm) cc_final: 0.7765 (tpt) REVERT: A 126 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 543 LYS cc_start: 0.9013 (tppt) cc_final: 0.8806 (mptt) REVERT: A 617 ASP cc_start: 0.7947 (t70) cc_final: 0.7614 (t0) REVERT: A 631 MET cc_start: 0.8492 (mmp) cc_final: 0.8281 (tpp) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.0921 time to fit residues: 15.1118 Evaluate side-chains 97 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 92 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 HIS A 354 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** 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 = 0.3794 r_free = 0.3794 target = 0.142722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106468 restraints weight = 19444.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105458 restraints weight = 12606.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105997 restraints weight = 13067.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107508 restraints weight = 7856.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107703 restraints weight = 6568.455| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12535 Z= 0.127 Angle : 0.481 6.218 17079 Z= 0.251 Chirality : 0.042 0.194 1837 Planarity : 0.004 0.051 2125 Dihedral : 7.661 115.340 1676 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.82 % Rotamer: Outliers : 1.15 % Allowed : 6.51 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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 (0.22), residues: 1465 helix: 1.87 (0.19), residues: 723 sheet: -1.34 (0.49), residues: 108 loop : 0.18 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.019 0.001 TYR A 118 PHE 0.014 0.001 PHE B 144 TRP 0.021 0.001 TRP B 223 HIS 0.008 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00298 (12534) covalent geometry : angle 0.48147 (17077) hydrogen bonds : bond 0.04696 ( 577) hydrogen bonds : angle 4.17861 ( 1626) link_MAN-THR : bond 0.00802 ( 1) link_MAN-THR : angle 0.05478 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 108 MET cc_start: 0.7993 (mmm) cc_final: 0.7685 (mtp) REVERT: A 80 ASP cc_start: 0.7418 (m-30) cc_final: 0.7175 (m-30) REVERT: A 108 MET cc_start: 0.8058 (mmm) cc_final: 0.7804 (tpt) REVERT: A 126 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 543 LYS cc_start: 0.8976 (tppt) cc_final: 0.8775 (mptt) REVERT: A 553 PHE cc_start: 0.8639 (m-10) cc_final: 0.8313 (m-80) REVERT: A 559 LEU cc_start: 0.8286 (tp) cc_final: 0.7891 (pp) REVERT: A 617 ASP cc_start: 0.7956 (t70) cc_final: 0.7733 (t0) outliers start: 15 outliers final: 11 residues processed: 116 average time/residue: 0.0867 time to fit residues: 15.4886 Evaluate side-chains 98 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 30 optimal weight: 10.0000 chunk 104 optimal weight: 40.0000 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 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 = 0.3770 r_free = 0.3770 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105343 restraints weight = 19600.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103384 restraints weight = 12365.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104006 restraints weight = 13615.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105229 restraints weight = 7686.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105839 restraints weight = 6421.806| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12535 Z= 0.157 Angle : 0.496 7.543 17079 Z= 0.256 Chirality : 0.042 0.157 1837 Planarity : 0.004 0.046 2125 Dihedral : 7.295 104.459 1674 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.15 % Allowed : 6.97 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.22 (0.22), residues: 1465 helix: 1.82 (0.19), residues: 721 sheet: -1.38 (0.46), residues: 120 loop : 0.18 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.018 0.001 TYR B 118 PHE 0.016 0.001 PHE A 642 TRP 0.018 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00378 (12534) covalent geometry : angle 0.49625 (17077) hydrogen bonds : bond 0.04899 ( 577) hydrogen bonds : angle 4.20035 ( 1626) link_MAN-THR : bond 0.00614 ( 1) link_MAN-THR : angle 0.20905 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: B 720 VAL cc_start: 0.9326 (t) cc_final: 0.9113 (m) REVERT: A 126 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 543 LYS cc_start: 0.8980 (tppt) cc_final: 0.8772 (mptt) REVERT: A 553 PHE cc_start: 0.8670 (m-10) cc_final: 0.8308 (m-80) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.0864 time to fit residues: 14.3745 Evaluate side-chains 100 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105665 restraints weight = 19457.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104300 restraints weight = 12380.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105313 restraints weight = 10824.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105894 restraints weight = 7314.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106592 restraints weight = 6512.312| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12535 Z= 0.110 Angle : 0.462 7.695 17079 Z= 0.239 Chirality : 0.041 0.136 1837 Planarity : 0.004 0.045 2125 Dihedral : 6.949 97.510 1674 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.00 % Allowed : 7.58 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.34 (0.22), residues: 1465 helix: 1.92 (0.19), residues: 723 sheet: -1.31 (0.47), residues: 119 loop : 0.21 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 366 TYR 0.017 0.001 TYR A 118 PHE 0.013 0.001 PHE B 290 TRP 0.016 0.001 TRP B 223 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00254 (12534) covalent geometry : angle 0.46219 (17077) hydrogen bonds : bond 0.04514 ( 577) hydrogen bonds : angle 4.07526 ( 1626) link_MAN-THR : bond 0.00578 ( 1) link_MAN-THR : angle 0.89126 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: B 108 MET cc_start: 0.7872 (mmm) cc_final: 0.7618 (mtp) REVERT: B 396 VAL cc_start: 0.8224 (t) cc_final: 0.7981 (m) REVERT: A 549 GLN cc_start: 0.9207 (mm110) cc_final: 0.8448 (mm-40) REVERT: A 553 PHE cc_start: 0.8652 (m-10) cc_final: 0.8093 (m-80) REVERT: A 559 LEU cc_start: 0.8245 (tp) cc_final: 0.8040 (pp) REVERT: A 617 ASP cc_start: 0.8035 (t70) cc_final: 0.7775 (t0) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.0916 time to fit residues: 16.1714 Evaluate side-chains 103 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103044 restraints weight = 19706.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101456 restraints weight = 13341.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102359 restraints weight = 12560.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102710 restraints weight = 7855.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104908 restraints weight = 6848.145| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12535 Z= 0.183 Angle : 0.514 7.735 17079 Z= 0.265 Chirality : 0.043 0.201 1837 Planarity : 0.004 0.042 2125 Dihedral : 7.037 86.366 1674 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.59 % Favored : 97.34 % Rotamer: Outliers : 1.30 % Allowed : 7.43 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.13 (0.22), residues: 1465 helix: 1.68 (0.19), residues: 727 sheet: -1.38 (0.46), residues: 119 loop : 0.19 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 366 TYR 0.026 0.001 TYR B 118 PHE 0.018 0.002 PHE A 642 TRP 0.017 0.001 TRP B 223 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00448 (12534) covalent geometry : angle 0.51345 (17077) hydrogen bonds : bond 0.05109 ( 577) hydrogen bonds : angle 4.26003 ( 1626) link_MAN-THR : bond 0.00663 ( 1) link_MAN-THR : angle 0.96010 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.453 Fit side-chains REVERT: B 108 MET cc_start: 0.7944 (mmm) cc_final: 0.7643 (mtp) REVERT: B 462 ASP cc_start: 0.8646 (t0) cc_final: 0.8371 (t0) outliers start: 17 outliers final: 15 residues processed: 107 average time/residue: 0.0920 time to fit residues: 15.3605 Evaluate side-chains 101 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 67 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS A 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105494 restraints weight = 19505.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104197 restraints weight = 12605.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104227 restraints weight = 14679.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106391 restraints weight = 7737.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106500 restraints weight = 5706.043| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12535 Z= 0.121 Angle : 0.493 16.729 17079 Z= 0.248 Chirality : 0.041 0.177 1837 Planarity : 0.004 0.044 2125 Dihedral : 6.762 78.012 1674 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.00 % Allowed : 8.27 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.28 (0.22), residues: 1465 helix: 1.83 (0.19), residues: 728 sheet: -1.27 (0.47), residues: 114 loop : 0.20 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 366 TYR 0.029 0.001 TYR B 118 PHE 0.010 0.001 PHE B 144 TRP 0.016 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00284 (12534) covalent geometry : angle 0.49243 (17077) hydrogen bonds : bond 0.04646 ( 577) hydrogen bonds : angle 4.12694 ( 1626) link_MAN-THR : bond 0.00512 ( 1) link_MAN-THR : angle 1.25354 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 108 MET cc_start: 0.7880 (mmm) cc_final: 0.7655 (mtp) REVERT: B 462 ASP cc_start: 0.8608 (t0) cc_final: 0.8304 (t0) REVERT: B 568 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 73 TYR cc_start: 0.8916 (t80) cc_final: 0.8567 (t80) REVERT: A 80 ASP cc_start: 0.7775 (t0) cc_final: 0.7494 (t0) REVERT: A 617 ASP cc_start: 0.8194 (t70) cc_final: 0.7881 (t0) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 0.0810 time to fit residues: 14.0748 Evaluate side-chains 104 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 40.0000 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS A 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105320 restraints weight = 19520.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104188 restraints weight = 12873.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105029 restraints weight = 11956.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105413 restraints weight = 7529.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107652 restraints weight = 6497.306| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12535 Z= 0.115 Angle : 0.488 15.586 17079 Z= 0.246 Chirality : 0.041 0.176 1837 Planarity : 0.004 0.044 2125 Dihedral : 6.608 75.384 1674 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 0.92 % Allowed : 8.27 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.33 (0.22), residues: 1465 helix: 1.86 (0.19), residues: 728 sheet: -1.23 (0.47), residues: 114 loop : 0.24 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 621 TYR 0.028 0.001 TYR B 118 PHE 0.010 0.001 PHE B 144 TRP 0.015 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00268 (12534) covalent geometry : angle 0.48760 (17077) hydrogen bonds : bond 0.04525 ( 577) hydrogen bonds : angle 4.09071 ( 1626) link_MAN-THR : bond 0.00542 ( 1) link_MAN-THR : angle 0.92851 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 108 MET cc_start: 0.7863 (mmm) cc_final: 0.7654 (mtp) REVERT: B 462 ASP cc_start: 0.8627 (t0) cc_final: 0.8315 (t0) REVERT: B 568 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 73 TYR cc_start: 0.8902 (t80) cc_final: 0.8445 (t80) REVERT: A 80 ASP cc_start: 0.7715 (t0) cc_final: 0.7490 (t0) REVERT: A 84 PHE cc_start: 0.9005 (m-80) cc_final: 0.8687 (m-80) REVERT: A 617 ASP cc_start: 0.8230 (t70) cc_final: 0.7924 (t0) outliers start: 12 outliers final: 11 residues processed: 108 average time/residue: 0.0872 time to fit residues: 15.1286 Evaluate side-chains 106 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 0.0060 chunk 94 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 40.0000 overall best weight: 1.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106482 restraints weight = 19725.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104225 restraints weight = 12044.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105076 restraints weight = 12132.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106186 restraints weight = 7609.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106663 restraints weight = 6366.735| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12535 Z= 0.112 Angle : 0.489 15.564 17079 Z= 0.246 Chirality : 0.041 0.173 1837 Planarity : 0.004 0.043 2125 Dihedral : 6.472 74.156 1674 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 0.84 % Allowed : 8.81 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.37 (0.22), residues: 1465 helix: 1.89 (0.19), residues: 728 sheet: -1.22 (0.47), residues: 114 loop : 0.26 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.030 0.001 TYR B 118 PHE 0.038 0.001 PHE A 718 TRP 0.015 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00257 (12534) covalent geometry : angle 0.48874 (17077) hydrogen bonds : bond 0.04445 ( 577) hydrogen bonds : angle 4.06973 ( 1626) link_MAN-THR : bond 0.00555 ( 1) link_MAN-THR : angle 0.91171 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 462 ASP cc_start: 0.8624 (t0) cc_final: 0.8324 (t0) REVERT: B 568 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 73 TYR cc_start: 0.8867 (t80) cc_final: 0.8437 (t80) REVERT: A 84 PHE cc_start: 0.8978 (m-80) cc_final: 0.8709 (m-80) REVERT: A 617 ASP cc_start: 0.8234 (t70) cc_final: 0.7945 (t0) outliers start: 11 outliers final: 11 residues processed: 104 average time/residue: 0.0963 time to fit residues: 15.5652 Evaluate side-chains 106 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain C residue 5 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.0070 chunk 131 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS A 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105905 restraints weight = 19537.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103443 restraints weight = 12080.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104435 restraints weight = 11349.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106351 restraints weight = 7368.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106336 restraints weight = 6107.475| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12535 Z= 0.126 Angle : 0.493 15.322 17079 Z= 0.248 Chirality : 0.041 0.170 1837 Planarity : 0.004 0.043 2125 Dihedral : 6.426 73.278 1674 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 0.84 % Allowed : 8.73 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 1.35 (0.22), residues: 1465 helix: 1.85 (0.19), residues: 730 sheet: -1.24 (0.47), residues: 114 loop : 0.29 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.027 0.001 TYR B 118 PHE 0.033 0.001 PHE A 718 TRP 0.015 0.001 TRP B 223 HIS 0.005 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00299 (12534) covalent geometry : angle 0.49269 (17077) hydrogen bonds : bond 0.04513 ( 577) hydrogen bonds : angle 4.07241 ( 1626) link_MAN-THR : bond 0.00507 ( 1) link_MAN-THR : angle 0.87038 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.81 seconds wall clock time: 30 minutes 2.07 seconds (1802.07 seconds total)