Starting phenix.real_space_refine
on Fri Aug 22 20:16:46 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xow_22282/08_2025/6xow_22282.cif"
  }
  resolution = 4.6
  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=   0.000 sd=   0.006
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: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4904      2.51       5
     N    1307      2.21       5
     O    1461      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7711
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7711
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7697
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7697
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 4, 'PTRANS': 60, 'TRANS': 901}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7872
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
    residue:
      pdb=" N  AASN A 915 " occ=0.59
      ... (14 atoms not shown)
      pdb=" ND2BASN A 915 " occ=0.41
  Time building chain proxies: 3.01, per 1000 atoms: 0.39
  Number of scatterers: 7711
  At special positions: 0
  Unit cell: (87.21, 87.21, 97.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1461      8.00
     N    1307      7.00
     C    4904      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 516.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      54.7% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 101 through 111
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.775A  pdb=" N   LYS A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 3.909A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.573A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.852A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 466 through 481
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 528
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 623 through 625
      No H-bonds generated for 'chain 'A' and resid 623 through 625'
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 3.865A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 787
      No H-bonds generated for 'chain 'A' and resid 785 through 787'
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 878 through 894
      removed outlier: 4.200A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 902
    Processing helix  chain 'A' and resid 928 through 945
      removed outlier: 3.512A  pdb=" N   LEU A 932 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 964
    Processing helix  chain 'A' and resid 973 through 980
      removed outlier: 3.808A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.693A  pdb=" N   LYS A 986 " --> pdb=" O   SER A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1009
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.227A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A  63 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ARG A  75 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   MET A 135 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   SER A 149 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.227A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A  63 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ARG A  75 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ARG A 505 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   ILE A 311 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   GLY A 392 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   PHE A 332 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   SER A 390 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   TYR A 388 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   ASP A 336 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   GLU A 386 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A 388 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 381 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER A 390 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 579
      removed outlier: 7.402A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 667 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 579
      removed outlier: 7.402A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.889A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1336 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: 1.22

  Time building geometry restraints manager: 0.90 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 2455
        1.33 -     1.45: 1286
        1.45 -     1.57: 4101
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7904
  Sorted by residual:
  bond pdb=" CG  ARG A 545 "
       pdb=" CD  ARG A 545 "
    ideal  model  delta    sigma   weight residual
    1.520  1.469  0.051 3.00e-02 1.11e+03 2.86e+00
  bond pdb=" CB  GLN A  91 "
       pdb=" CG  GLN A  91 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.45e+00
  bond pdb=" N   ILE A 724 "
       pdb=" CA  ILE A 724 "
    ideal  model  delta    sigma   weight residual
    1.460  1.443  0.017 1.21e-02 6.83e+03 1.87e+00
  bond pdb=" CA  GLY A 644 "
       pdb=" C   GLY A 644 "
    ideal  model  delta    sigma   weight residual
    1.514  1.496  0.019 1.41e-02 5.03e+03 1.74e+00
  bond pdb=" CA  THR A 144 "
       pdb=" CB  THR A 144 "
    ideal  model  delta    sigma   weight residual
    1.532  1.508  0.024 1.82e-02 3.02e+03 1.69e+00
  ... (remaining 7899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 10344
        2.31 -     4.61: 306
        4.61 -     6.92: 57
        6.92 -     9.23: 10
        9.23 -    11.53: 3
  Bond angle restraints: 10720
  Sorted by residual:
  angle pdb=" C   TYR A 614 "
        pdb=" N   VAL A 615 "
        pdb=" CA  VAL A 615 "
      ideal   model   delta    sigma   weight residual
     120.24  123.48   -3.24 6.30e-01 2.52e+00 2.64e+01
  angle pdb=" C   ILE A 899 "
        pdb=" N   ARG A 900 "
        pdb=" CA  ARG A 900 "
      ideal   model   delta    sigma   weight residual
     120.88  114.63    6.25 1.62e+00 3.81e-01 1.49e+01
  angle pdb=" CB  MET A 749 "
        pdb=" CG  MET A 749 "
        pdb=" SD  MET A 749 "
      ideal   model   delta    sigma   weight residual
     112.70  101.17   11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" CA  TYR A 492 "
        pdb=" CB  TYR A 492 "
        pdb=" CG  TYR A 492 "
      ideal   model   delta    sigma   weight residual
     113.90  107.22    6.68 1.80e+00 3.09e-01 1.38e+01
  angle pdb=" N   GLU A 709 "
        pdb=" CA  GLU A 709 "
        pdb=" CB  GLU A 709 "
      ideal   model   delta    sigma   weight residual
     110.16  115.32   -5.16 1.48e+00 4.57e-01 1.21e+01
  ... (remaining 10715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4413
       17.91 -    35.83: 294
       35.83 -    53.74: 46
       53.74 -    71.65: 18
       71.65 -    89.56: 10
  Dihedral angle restraints: 4781
    sinusoidal: 1955
      harmonic: 2826
  Sorted by residual:
  dihedral pdb=" CA  ALA A 319 "
           pdb=" C   ALA A 319 "
           pdb=" N   THR A 320 "
           pdb=" CA  THR A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  GLN A 394 "
           pdb=" C   GLN A 394 "
           pdb=" N   GLY A 395 "
           pdb=" CA  GLY A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ARG A 129 "
           pdb=" C   ARG A 129 "
           pdb=" N   SER A 130 "
           pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 4778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 733
       0.044 -    0.089: 324
       0.089 -    0.133: 100
       0.133 -    0.177: 15
       0.177 -    0.222: 2
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  TYR A 163 "
            pdb=" N   TYR A 163 "
            pdb=" C   TYR A 163 "
            pdb=" CB  TYR A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  ILE A1020 "
            pdb=" CA  ILE A1020 "
            pdb=" CG1 ILE A1020 "
            pdb=" CG2 ILE A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.17e-01
  chirality pdb=" CA  LYS A 437 "
            pdb=" N   LYS A 437 "
            pdb=" C   LYS A 437 "
            pdb=" CB  LYS A 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 303 "   -0.033 2.00e-02 2.50e+03   2.63e-02 1.73e+01
        pdb=" CG  TRP A 303 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 303 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 303 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 303 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 303 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 303 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 303 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 303 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 314 "   -0.065 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO A 315 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 242 "    0.050 5.00e-02 4.00e+02   7.58e-02 9.20e+00
        pdb=" N   PRO A 243 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 243 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 243 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1398 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 117
        2.57 -     3.15: 7115
        3.15 -     3.74: 12800
        3.74 -     4.32: 17159
        4.32 -     4.90: 26933
  Nonbonded interactions: 64124
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 872 "
            pdb=" O   GLY A 916 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" O   ASP A 377 "
            pdb=" OG  SER A 390 "
     model   vdw
     2.033 3.040
  nonbonded pdb=" OD2 ASP A 336 "
            pdb=" OG1 THR A 338 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" ND1 HIS A 186 "
            pdb=" O   THR A 194 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" O   ILE A 803 "
            pdb=" NH1 ARG A 805 "
     model   vdw
     2.089 3.120
  ... (remaining 64119 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.41 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:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.890
  Find NCS groups from input model:        0.030
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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      :  0.006   0.051   7904  Z= 0.306
  Angle     :  0.998  11.533  10720  Z= 0.543
  Chirality :  0.053   0.222   1174
  Planarity :  0.007   0.098   1401
  Dihedral  : 13.389  89.563   2953
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 24.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.26), residues: 968
  helix: -0.40 (0.22), residues: 458
  sheet:  0.30 (0.38), residues: 176
  loop : -1.35 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG A 410 
 TYR   0.032   0.003   TYR A 597 
 PHE   0.024   0.003   PHE A 138 
 TRP   0.069   0.006   TRP A 303 
 HIS   0.012   0.002   HIS A 498 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 7904)
  covalent geometry    : angle       0.99790 (10720)
  hydrogen bonds       : bond        0.19946 (  429)
  hydrogen bonds       : angle       8.10319 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.7623 (t80) cc_final: 0.7296 (t80)
REVERT: A  266 PHE cc_start: 0.7046 (t80) cc_final: 0.6057 (t80)
REVERT: A  436 MET cc_start: 0.9288 (mtp) cc_final: 0.8949 (mtt)
REVERT: A  454 CYS cc_start: 0.8124 (t) cc_final: 0.7782 (p)
REVERT: A  667 LEU cc_start: 0.9016 (tp) cc_final: 0.8585 (tp)
REVERT: A  702 LEU cc_start: 0.9307 (mt) cc_final: 0.9061 (pp)
REVERT: A  917 ILE cc_start: 0.7541 (mm) cc_final: 0.7304 (mm)
REVERT: A  985 MET cc_start: 0.7967 (mpp) cc_final: 0.6747 (mpp)
REVERT: A 1037 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7224 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0806
  time to fit residues: 14.6981
Evaluate side-chains
  77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0060
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.8004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN
A 495 ASN
A 524 GLN
A 536 GLN
A 976 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.079029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.064757 restraints weight = 163380.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.066891 restraints weight = 68396.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.068275 restraints weight = 39722.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.069183 restraints weight = 26651.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.069783 restraints weight = 19743.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7904  Z= 0.167
  Angle     :  0.781   9.199  10720  Z= 0.409
  Chirality :  0.048   0.233   1174
  Planarity :  0.007   0.082   1401
  Dihedral  :  5.512  19.937   1039
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.56 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.27), residues: 968
  helix:  0.48 (0.23), residues: 464
  sheet:  0.38 (0.39), residues: 176
  loop : -1.14 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 410 
 TYR   0.029   0.002   TYR A 597 
 PHE   0.022   0.002   PHE A 935 
 TRP   0.034   0.003   TRP A 303 
 HIS   0.009   0.001   HIS A 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7904)
  covalent geometry    : angle       0.78134 (10720)
  hydrogen bonds       : bond        0.04951 (  429)
  hydrogen bonds       : angle       5.69211 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9582 (t80) cc_final: 0.9141 (t80)
REVERT: A  135 MET cc_start: 0.7928 (pmm) cc_final: 0.7723 (pmm)
REVERT: A  265 PHE cc_start: 0.9832 (m-80) cc_final: 0.9569 (m-80)
REVERT: A  318 PHE cc_start: 0.9601 (p90) cc_final: 0.9342 (p90)
REVERT: A  354 THR cc_start: 0.8583 (p) cc_final: 0.8254 (p)
REVERT: A  361 PHE cc_start: 0.9760 (m-10) cc_final: 0.9507 (m-80)
REVERT: A  437 LYS cc_start: 0.9729 (mptt) cc_final: 0.9467 (pttt)
REVERT: A  454 CYS cc_start: 0.9861 (t) cc_final: 0.9611 (p)
REVERT: A  595 MET cc_start: 0.9693 (ptp) cc_final: 0.9297 (ptt)
REVERT: A  598 PHE cc_start: 0.9244 (t80) cc_final: 0.8690 (t80)
REVERT: A  702 LEU cc_start: 0.9709 (mt) cc_final: 0.9462 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0737
  time to fit residues: 11.7902
Evaluate side-chains
  79 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0000
   chunk 10 optimal weight:   10.0000
   chunk 79 optimal weight:   30.0000
   chunk 1 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    6.3992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 HIS
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.045140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.032621 restraints weight = 210113.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.034206 restraints weight = 116264.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.035374 restraints weight = 79955.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.036279 restraints weight = 60905.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.036945 restraints weight = 49605.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7904  Z= 0.203
  Angle     :  0.742   9.765  10720  Z= 0.388
  Chirality :  0.046   0.223   1174
  Planarity :  0.006   0.073   1401
  Dihedral  :  5.299  18.243   1039
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 20.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.68 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.27), residues: 968
  helix:  0.46 (0.23), residues: 466
  sheet:  0.24 (0.39), residues: 173
  loop : -1.01 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 173 
 TYR   0.027   0.002   TYR A 597 
 PHE   0.032   0.002   PHE A 217 
 TRP   0.028   0.003   TRP A 303 
 HIS   0.009   0.002   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 7904)
  covalent geometry    : angle       0.74206 (10720)
  hydrogen bonds       : bond        0.04257 (  429)
  hydrogen bonds       : angle       5.59598 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9340 (t80) cc_final: 0.8735 (t80)
REVERT: A  135 MET cc_start: 0.8212 (pmm) cc_final: 0.7980 (pmm)
REVERT: A  265 PHE cc_start: 0.9638 (m-80) cc_final: 0.9317 (m-80)
REVERT: A  361 PHE cc_start: 0.9611 (m-80) cc_final: 0.8959 (m-80)
REVERT: A  433 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9421 (mm-30)
REVERT: A  918 PHE cc_start: 0.9609 (t80) cc_final: 0.9351 (t80)
REVERT: A 1037 ARG cc_start: 0.8852 (mmt90) cc_final: 0.8370 (mmt90)
  outliers start: 1
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0725
  time to fit residues: 10.3330
Evaluate side-chains
  67 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.048502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.033342 restraints weight = 220128.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.035498 restraints weight = 89464.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.037159 restraints weight = 53370.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.038375 restraints weight = 36986.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.039295 restraints weight = 28181.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5543
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7904  Z= 0.184
  Angle     :  0.715   8.714  10720  Z= 0.374
  Chirality :  0.046   0.226   1174
  Planarity :  0.006   0.067   1401
  Dihedral  :  5.167  16.950   1039
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 21.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.86 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.27), residues: 968
  helix:  0.52 (0.23), residues: 467
  sheet:  0.10 (0.38), residues: 173
  loop : -0.93 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 505 
 TYR   0.021   0.002   TYR A 492 
 PHE   0.015   0.002   PHE A 935 
 TRP   0.018   0.002   TRP A 303 
 HIS   0.006   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7904)
  covalent geometry    : angle       0.71486 (10720)
  hydrogen bonds       : bond        0.03955 (  429)
  hydrogen bonds       : angle       5.44628 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 PHE cc_start: 0.8725 (p90) cc_final: 0.8440 (p90)
REVERT: A  344 PHE cc_start: 0.9068 (t80) cc_final: 0.8841 (t80)
REVERT: A  361 PHE cc_start: 0.9652 (m-80) cc_final: 0.9368 (m-80)
REVERT: A  464 LEU cc_start: 0.8498 (mt) cc_final: 0.8227 (mp)
REVERT: A  598 PHE cc_start: 0.9574 (t80) cc_final: 0.9005 (t80)
REVERT: A  710 LEU cc_start: 0.8415 (mt) cc_final: 0.8035 (tt)
REVERT: A  714 ILE cc_start: 0.6632 (mt) cc_final: 0.5240 (mt)
REVERT: A  724 ILE cc_start: 0.5313 (pt) cc_final: 0.4835 (pt)
REVERT: A  853 MET cc_start: 0.8298 (mpp) cc_final: 0.8092 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0660
  time to fit residues: 8.9348
Evaluate side-chains
  67 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0470
   chunk 82 optimal weight:    8.9990
   chunk 62 optimal weight:   40.0000
   chunk 26 optimal weight:    0.0070
   chunk 10 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 83 optimal weight:   40.0000
   chunk 71 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   overall best weight:    5.4102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** 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 = 0.3113 r_free = 0.3113 target = 0.047755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.033030 restraints weight = 201736.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.035056 restraints weight = 88621.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.036625 restraints weight = 54484.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037799 restraints weight = 38670.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.038717 restraints weight = 29735.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5918
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7904  Z= 0.175
  Angle     :  0.710   9.904  10720  Z= 0.368
  Chirality :  0.045   0.159   1174
  Planarity :  0.006   0.066   1401
  Dihedral  :  5.107  19.027   1039
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.93 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.27), residues: 968
  helix:  0.51 (0.23), residues: 471
  sheet:  0.10 (0.38), residues: 167
  loop : -0.77 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1037 
 TYR   0.023   0.002   TYR A 492 
 PHE   0.021   0.002   PHE A 124 
 TRP   0.017   0.002   TRP A 684 
 HIS   0.006   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7904)
  covalent geometry    : angle       0.71041 (10720)
  hydrogen bonds       : bond        0.03821 (  429)
  hydrogen bonds       : angle       5.35457 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 PHE cc_start: 0.9194 (t80) cc_final: 0.8944 (t80)
REVERT: A  361 PHE cc_start: 0.9725 (m-80) cc_final: 0.9342 (m-80)
REVERT: A  428 LEU cc_start: 0.9135 (mp) cc_final: 0.8894 (mt)
REVERT: A  598 PHE cc_start: 0.9432 (t80) cc_final: 0.8986 (t80)
REVERT: A  714 ILE cc_start: 0.6531 (mt) cc_final: 0.6291 (mt)
REVERT: A  724 ILE cc_start: 0.5246 (pt) cc_final: 0.4915 (pt)
REVERT: A  743 MET cc_start: 0.8954 (tpp) cc_final: 0.8673 (mmm)
REVERT: A  918 PHE cc_start: 0.9308 (t80) cc_final: 0.9108 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0624
  time to fit residues: 8.0080
Evaluate side-chains
  67 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 74 optimal weight:   30.0000
   chunk 68 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    3.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 ASN
A 276 HIS
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** 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 = 0.2944 r_free = 0.2944 target = 0.044341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.031890 restraints weight = 192697.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.033479 restraints weight = 109377.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.034731 restraints weight = 75352.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.035619 restraints weight = 57428.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.036304 restraints weight = 46622.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7904  Z= 0.143
  Angle     :  0.666   8.325  10720  Z= 0.344
  Chirality :  0.044   0.157   1174
  Planarity :  0.006   0.066   1401
  Dihedral  :  5.025  29.089   1039
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.21 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.27), residues: 968
  helix:  0.71 (0.24), residues: 471
  sheet:  0.12 (0.39), residues: 167
  loop : -0.69 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1037 
 TYR   0.017   0.001   TYR A 597 
 PHE   0.016   0.002   PHE A 124 
 TRP   0.011   0.001   TRP A 303 
 HIS   0.011   0.001   HIS A 856 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7904)
  covalent geometry    : angle       0.66555 (10720)
  hydrogen bonds       : bond        0.03582 (  429)
  hydrogen bonds       : angle       5.28253 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 PHE cc_start: 0.9613 (m-80) cc_final: 0.9367 (m-80)
REVERT: A  361 PHE cc_start: 0.9632 (m-80) cc_final: 0.8879 (m-80)
REVERT: A  598 PHE cc_start: 0.8920 (t80) cc_final: 0.8709 (t80)
REVERT: A  705 MET cc_start: 0.9005 (ptp) cc_final: 0.8795 (ptp)
REVERT: A  749 MET cc_start: 0.9452 (ppp) cc_final: 0.9184 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0567
  time to fit residues: 7.5060
Evaluate side-chains
  64 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:   30.0000
   chunk 46 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 78 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 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 = 0.2910 r_free = 0.2910 target = 0.042653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.030049 restraints weight = 239707.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.031681 restraints weight = 124467.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.032977 restraints weight = 82945.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.033926 restraints weight = 62044.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.034640 restraints weight = 49784.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7904  Z= 0.172
  Angle     :  0.698   8.451  10720  Z= 0.367
  Chirality :  0.044   0.164   1174
  Planarity :  0.006   0.067   1401
  Dihedral  :  5.111  36.917   1039
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.40 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.28), residues: 968
  helix:  0.63 (0.24), residues: 471
  sheet: -0.02 (0.39), residues: 170
  loop : -0.54 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 173 
 TYR   0.021   0.002   TYR A 492 
 PHE   0.019   0.002   PHE A 124 
 TRP   0.017   0.002   TRP A 684 
 HIS   0.009   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7904)
  covalent geometry    : angle       0.69759 (10720)
  hydrogen bonds       : bond        0.03654 (  429)
  hydrogen bonds       : angle       5.47262 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9223 (t80) cc_final: 0.8860 (t80)
REVERT: A  265 PHE cc_start: 0.9518 (m-80) cc_final: 0.9090 (m-80)
REVERT: A  353 LEU cc_start: 0.9765 (mt) cc_final: 0.9550 (mt)
REVERT: A  361 PHE cc_start: 0.9616 (m-80) cc_final: 0.8801 (m-80)
REVERT: A  705 MET cc_start: 0.8987 (ptp) cc_final: 0.8775 (ptp)
REVERT: A  749 MET cc_start: 0.9517 (ppp) cc_final: 0.9198 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0642
  time to fit residues: 8.2718
Evaluate side-chains
  61 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 93 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN
A 262 ASN
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 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 = 0.2882 r_free = 0.2882 target = 0.041760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.030096 restraints weight = 186092.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.031499 restraints weight = 109747.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.032606 restraints weight = 77556.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.033410 restraints weight = 59981.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.034010 restraints weight = 49472.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7904  Z= 0.212
  Angle     :  0.746   8.570  10720  Z= 0.392
  Chirality :  0.046   0.159   1174
  Planarity :  0.006   0.067   1401
  Dihedral  :  5.407  46.532   1039
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 22.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.58 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.27), residues: 968
  helix:  0.44 (0.24), residues: 467
  sheet: -0.21 (0.38), residues: 174
  loop : -0.57 (0.38), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 505 
 TYR   0.027   0.002   TYR A 492 
 PHE   0.018   0.002   PHE A 169 
 TRP   0.014   0.002   TRP A 303 
 HIS   0.010   0.002   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 7904)
  covalent geometry    : angle       0.74639 (10720)
  hydrogen bonds       : bond        0.03780 (  429)
  hydrogen bonds       : angle       5.64144 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9269 (t80) cc_final: 0.8911 (t80)
REVERT: A  265 PHE cc_start: 0.9426 (m-80) cc_final: 0.8909 (m-80)
REVERT: A  344 PHE cc_start: 0.9518 (t80) cc_final: 0.9197 (t80)
REVERT: A  353 LEU cc_start: 0.9772 (mt) cc_final: 0.9566 (mt)
REVERT: A  361 PHE cc_start: 0.9619 (m-80) cc_final: 0.9073 (m-80)
REVERT: A  778 MET cc_start: 0.8767 (tpt) cc_final: 0.8397 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0548
  time to fit residues: 7.1914
Evaluate side-chains
  62 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:   30.0000
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    4.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN
** A 771 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 = 0.2921 r_free = 0.2921 target = 0.042901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.030656 restraints weight = 192723.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.032182 restraints weight = 110134.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.033330 restraints weight = 76428.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.034205 restraints weight = 58758.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.034849 restraints weight = 48165.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.5083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7904  Z= 0.152
  Angle     :  0.687   8.279  10720  Z= 0.356
  Chirality :  0.045   0.153   1174
  Planarity :  0.005   0.063   1401
  Dihedral  :  5.237  48.985   1039
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.28), residues: 968
  helix:  0.60 (0.24), residues: 465
  sheet: -0.25 (0.39), residues: 172
  loop : -0.48 (0.38), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 173 
 TYR   0.019   0.002   TYR A 597 
 PHE   0.015   0.002   PHE A 935 
 TRP   0.009   0.001   TRP A 303 
 HIS   0.010   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7904)
  covalent geometry    : angle       0.68740 (10720)
  hydrogen bonds       : bond        0.03465 (  429)
  hydrogen bonds       : angle       5.43481 ( 1336)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9231 (t80) cc_final: 0.8847 (t80)
REVERT: A  265 PHE cc_start: 0.9493 (m-80) cc_final: 0.8996 (m-80)
REVERT: A  344 PHE cc_start: 0.9475 (t80) cc_final: 0.9252 (t80)
REVERT: A  361 PHE cc_start: 0.9620 (m-80) cc_final: 0.9090 (m-80)
REVERT: A  640 GLU cc_start: 0.9519 (pt0) cc_final: 0.9162 (tp30)
REVERT: A  680 MET cc_start: 0.9557 (ppp) cc_final: 0.9352 (ppp)
REVERT: A  724 ILE cc_start: 0.8238 (pt) cc_final: 0.7995 (pt)
REVERT: A  743 MET cc_start: 0.9392 (mmp) cc_final: 0.8941 (mpp)
REVERT: A  749 MET cc_start: 0.9545 (ppp) cc_final: 0.9312 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0682
  time to fit residues: 8.5642
Evaluate side-chains
  64 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 94 optimal weight:    0.0270
   chunk 54 optimal weight:   40.0000
   chunk 59 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 15 optimal weight:   20.0000
   chunk 16 optimal weight:    0.7980
   overall best weight:    3.9644

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 GLN
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 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 = 0.2924 r_free = 0.2924 target = 0.042929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.030005 restraints weight = 257514.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.031637 restraints weight = 130564.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.032932 restraints weight = 86436.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.033929 restraints weight = 64470.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.034625 restraints weight = 51587.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.5233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7904  Z= 0.144
  Angle     :  0.684   7.988  10720  Z= 0.352
  Chirality :  0.045   0.154   1174
  Planarity :  0.005   0.078   1401
  Dihedral  :  5.158  48.162   1039
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.28), residues: 968
  helix:  0.67 (0.24), residues: 467
  sheet: -0.29 (0.39), residues: 172
  loop : -0.43 (0.38), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 173 
 TYR   0.019   0.002   TYR A 597 
 PHE   0.015   0.002   PHE A 124 
 TRP   0.013   0.002   TRP A 303 
 HIS   0.009   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7904)
  covalent geometry    : angle       0.68353 (10720)
  hydrogen bonds       : bond        0.03379 (  429)
  hydrogen bonds       : angle       5.35643 ( 1336)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 PHE cc_start: 0.9189 (t80) cc_final: 0.8810 (t80)
REVERT: A  265 PHE cc_start: 0.9458 (m-80) cc_final: 0.8955 (m-80)
REVERT: A  344 PHE cc_start: 0.9539 (t80) cc_final: 0.9278 (t80)
REVERT: A  361 PHE cc_start: 0.9621 (m-80) cc_final: 0.9141 (m-80)
REVERT: A  680 MET cc_start: 0.9543 (ppp) cc_final: 0.9331 (ppp)
REVERT: A  743 MET cc_start: 0.9400 (mmp) cc_final: 0.9171 (mmm)
REVERT: A  749 MET cc_start: 0.9520 (ppp) cc_final: 0.9256 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0636
  time to fit residues: 8.3791
Evaluate side-chains
  63 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0870
   chunk 38 optimal weight:    7.9990
   overall best weight:    3.4164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 676 ASN ** 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 = 0.2929 r_free = 0.2929 target = 0.043073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.030287 restraints weight = 234984.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.031900 restraints weight = 123026.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.033161 restraints weight = 82688.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.034124 restraints weight = 62131.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.034832 restraints weight = 50170.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.5354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7904  Z= 0.134
  Angle     :  0.674   7.883  10720  Z= 0.346
  Chirality :  0.044   0.156   1174
  Planarity :  0.006   0.076   1401
  Dihedral  :  5.069  48.291   1039
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.12 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.44 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.28), residues: 968
  helix:  0.74 (0.24), residues: 468
  sheet: -0.26 (0.39), residues: 172
  loop : -0.33 (0.38), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 307 
 TYR   0.019   0.001   TYR A 597 
 PHE   0.014   0.002   PHE A 318 
 TRP   0.011   0.001   TRP A 303 
 HIS   0.009   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7904)
  covalent geometry    : angle       0.67403 (10720)
  hydrogen bonds       : bond        0.03270 (  429)
  hydrogen bonds       : angle       5.28187 ( 1336)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1228.83 seconds
wall clock time: 22 minutes 15.65 seconds (1335.65 seconds total)