Starting phenix.real_space_refine
on Wed Mar 12 10:39:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xov_22281/03_2025/6xov_22281.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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    4935      2.51       5
     N    1313      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7755
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7713
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7699
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7699
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7874
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 27
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 15
          Classifications: {'peptide': 3}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'UNK:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
  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: 8.69, per 1000 atoms: 1.12
  Number of scatterers: 7755
  At special positions: 0
  Unit cell: (86.355, 88.065, 98.325, 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    1468      8.00
     N    1313      7.00
     C    4935      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      52.2% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 201 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
      removed outlier: 3.617A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    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 282
      removed outlier: 4.270A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 366 through 369
      removed outlier: 3.748A  pdb=" N   GLY A 369 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 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
    Processing helix  chain 'A' and resid 442 through 456
      removed outlier: 5.376A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
      removed outlier: 3.547A  pdb=" N   LYS A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.674A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 527
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 608 through 612
      removed outlier: 3.574A  pdb=" N   LEU A 611 " --> pdb=" O   PRO A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 623
      removed outlier: 4.553A  pdb=" N   THR A 623 " --> pdb=" O   CYS A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 696 through 713
      removed outlier: 3.678A  pdb=" N   GLY A 713 " --> pdb=" O   GLU A 709 " (cutoff:3.500A)
    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 728
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.758A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   MET A 755 " --> pdb=" O   ARG A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 4.120A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 877 through 894
      removed outlier: 3.775A  pdb=" N   ALA A 881 " --> pdb=" O   ASP A 877 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE A 885 " --> pdb=" O   ALA A 881 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 899
    Processing helix  chain 'A' and resid 928 through 944
      removed outlier: 3.516A  pdb=" N   VAL A 939 " --> pdb=" O   PHE A 935 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP A 940 " --> pdb=" O   GLY A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 963
      removed outlier: 3.813A  pdb=" N   ILE A 952 " --> pdb=" O   THR A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 979
      removed outlier: 3.763A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.526A  pdb=" N   PHE A 994 " --> pdb=" O   ARG A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1009
      removed outlier: 3.509A  pdb=" N   ASP A1006 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ARG A1007 " --> pdb=" O   ALA A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1031
      removed outlier: 3.671A  pdb=" N   ASP A1031 " --> pdb=" O   LYS A1027 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.714A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A  53 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.714A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A  53 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 185
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313
      removed outlier: 7.175A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578
    Processing sheet with id=AA6, first strand: chain 'A' and resid 588 through 589
      removed outlier: 5.474A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER A 649 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 589
      removed outlier: 5.474A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.557A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   ASN A 864 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY A1017 " --> pdb=" O   CYS A 869 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1210 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1906
        1.33 -     1.45: 1564
        1.45 -     1.57: 4416
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7948
  Sorted by residual:
  bond pdb=" N   PHE A 318 "
       pdb=" CA  PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.026 1.29e-02 6.01e+03 4.12e+00
  bond pdb=" C   ILE A 242 "
       pdb=" N   PRO A 243 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.08e-02 8.57e+03 3.49e+00
  bond pdb=" CA  PHE A 318 "
       pdb=" C   PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.34e-02 5.57e+03 2.04e+00
  bond pdb=" N   GLY A 626 "
       pdb=" CA  GLY A 626 "
    ideal  model  delta    sigma   weight residual
    1.449  1.470 -0.020 1.45e-02 4.76e+03 1.98e+00
  bond pdb=" CB  ASN A 136 "
       pdb=" CG  ASN A 136 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.73e+00
  ... (remaining 7943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 10604
        2.48 -     4.96: 149
        4.96 -     7.45: 20
        7.45 -     9.93: 3
        9.93 -    12.41: 1
  Bond angle restraints: 10777
  Sorted by residual:
  angle pdb=" N   PHE A 318 "
        pdb=" CA  PHE A 318 "
        pdb=" C   PHE A 318 "
      ideal   model   delta    sigma   weight residual
     110.80  123.21  -12.41 2.13e+00 2.20e-01 3.39e+01
  angle pdb=" C   SER A 317 "
        pdb=" CA  SER A 317 "
        pdb=" CB  SER A 317 "
      ideal   model   delta    sigma   weight residual
     109.90  118.86   -8.96 1.56e+00 4.11e-01 3.30e+01
  angle pdb=" N   LYS A 324 "
        pdb=" CA  LYS A 324 "
        pdb=" C   LYS A 324 "
      ideal   model   delta    sigma   weight residual
     108.56  117.67   -9.11 1.74e+00 3.30e-01 2.74e+01
  angle pdb=" C   ASP A 321 "
        pdb=" N   PRO A 322 "
        pdb=" CA  PRO A 322 "
      ideal   model   delta    sigma   weight residual
     119.28  124.67   -5.39 1.10e+00 8.26e-01 2.41e+01
  angle pdb=" N   ILE A 758 "
        pdb=" CA  ILE A 758 "
        pdb=" C   ILE A 758 "
      ideal   model   delta    sigma   weight residual
     112.17  108.46    3.71 9.50e-01 1.11e+00 1.52e+01
  ... (remaining 10772 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4339
       17.82 -    35.64: 381
       35.64 -    53.46: 62
       53.46 -    71.27: 12
       71.27 -    89.09: 8
  Dihedral angle restraints: 4802
    sinusoidal: 1960
      harmonic: 2842
  Sorted by residual:
  dihedral pdb=" C   PHE A 318 "
           pdb=" N   PHE A 318 "
           pdb=" CA  PHE A 318 "
           pdb=" CB  PHE A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.25   12.65     0      2.50e+00 1.60e-01 2.56e+01
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   THR A 211 "
           pdb=" CA  THR A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.34   24.66     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" N   PHE A 318 "
           pdb=" C   PHE A 318 "
           pdb=" CA  PHE A 318 "
           pdb=" CB  PHE A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.48  -11.68     0      2.50e+00 1.60e-01 2.18e+01
  ... (remaining 4799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1156
       0.110 -    0.220: 23
       0.220 -    0.330: 1
       0.330 -    0.440: 0
       0.440 -    0.550: 1
  Chirality restraints: 1181
  Sorted by residual:
  chirality pdb=" CA  PHE A 318 "
            pdb=" N   PHE A 318 "
            pdb=" C   PHE A 318 "
            pdb=" CB  PHE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.57e+00
  chirality pdb=" CA  THR A 876 "
            pdb=" N   THR A 876 "
            pdb=" C   THR A 876 "
            pdb=" CB  THR A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  LYS A 324 "
            pdb=" N   LYS A 324 "
            pdb=" C   LYS A 324 "
            pdb=" CB  LYS A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 1178 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 163 "   -0.027 2.00e-02 2.50e+03   1.76e-02 6.17e+00
        pdb=" CG  TYR A 163 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 163 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 163 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 163 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 163 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 163 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 163 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 146 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   TYR A 146 "    0.032 2.00e-02 2.50e+03
        pdb=" O   TYR A 146 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PRO A 147 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 102 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO A 103 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 103 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 103 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 160
        2.66 -     3.22: 7612
        3.22 -     3.78: 12070
        3.78 -     4.34: 16710
        4.34 -     4.90: 27480
  Nonbonded interactions: 64032
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 373 "
            pdb=" N   PHE A 374 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   LEU A 365 "
            pdb=" OG  SER A 368 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER A 997 "
            pdb=" OD1 ASP A 999 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG1 THR A  50 "
            pdb=" OD1 ASP A  70 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OH  TYR A 538 "
     model   vdw
     2.235 3.040
  ... (remaining 64027 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     29.140
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.060
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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      :  0.005   0.044   7948  Z= 0.296
  Angle     :  0.758  12.411  10777  Z= 0.433
  Chirality :  0.048   0.550   1181
  Planarity :  0.006   0.045   1407
  Dihedral  : 14.282  89.092   2962
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.58 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.27), residues: 969
  helix: -0.29 (0.25), residues: 444
  sheet: -2.18 (0.37), residues: 174
  loop : -1.91 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 455 
 HIS   0.010   0.001   HIS A 108 
 PHE   0.022   0.002   PHE B  20 
 TYR   0.041   0.002   TYR A 163 
 ARG   0.004   0.000   ARG A 725 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 TYR cc_start: 0.8126 (t80) cc_final: 0.7824 (t80)
REVERT: A  106 LEU cc_start: 0.8882 (tp) cc_final: 0.8531 (tp)
REVERT: A  517 VAL cc_start: 0.8318 (p) cc_final: 0.8008 (p)
REVERT: A  520 THR cc_start: 0.8784 (m) cc_final: 0.8509 (p)
REVERT: A  884 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8566 (tppt)
REVERT: A  925 ASP cc_start: 0.7173 (t0) cc_final: 0.6894 (t0)
REVERT: A  953 ASP cc_start: 0.7911 (t70) cc_final: 0.7687 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1953
  time to fit residues: 25.9509
Evaluate side-chains
  66 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 GLN
A 552 GLN
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 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 = 0.3365 r_free = 0.3365 target = 0.072846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.058118 restraints weight = 58638.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 6.16
r_work: 0.2839 rms_B_bonded: 5.99 restraints_weight: 2.0000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7948  Z= 0.209
  Angle     :  0.665   9.042  10777  Z= 0.341
  Chirality :  0.044   0.204   1181
  Planarity :  0.006   0.048   1407
  Dihedral  :  5.065  45.022   1043
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.96 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.28), residues: 969
  helix:  0.58 (0.25), residues: 462
  sheet: -1.55 (0.39), residues: 166
  loop : -1.49 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 851 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.011   0.001   PHE A 344 
 TYR   0.018   0.002   TYR A 163 
 ARG   0.011   0.001   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A  604 LEU cc_start: 0.8795 (mt) cc_final: 0.8567 (mt)
REVERT: A  640 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8292 (mp0)
REVERT: A  755 MET cc_start: 0.8076 (mtm) cc_final: 0.7313 (ptp)
REVERT: A  792 THR cc_start: 0.9365 (m) cc_final: 0.9162 (p)
REVERT: A  884 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8359 (tppt)
REVERT: A  917 ILE cc_start: 0.8840 (mm) cc_final: 0.8631 (mm)
REVERT: A  925 ASP cc_start: 0.8471 (t0) cc_final: 0.7721 (t0)
REVERT: A  953 ASP cc_start: 0.8357 (t70) cc_final: 0.8059 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.1704
  time to fit residues: 21.0804
Evaluate side-chains
  76 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  985 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 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 = 0.3350 r_free = 0.3350 target = 0.071868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.057145 restraints weight = 63637.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 6.31
r_work: 0.2821 rms_B_bonded: 6.10 restraints_weight: 2.0000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7948  Z= 0.232
  Angle     :  0.617   8.666  10777  Z= 0.316
  Chirality :  0.043   0.189   1181
  Planarity :  0.005   0.047   1407
  Dihedral  :  4.865  41.798   1043
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.47 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 969
  helix:  0.83 (0.24), residues: 472
  sheet: -1.15 (0.39), residues: 168
  loop : -1.16 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 455 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.027   0.002   PHE A 389 
 TYR   0.013   0.002   TYR A 163 
 ARG   0.006   0.000   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A  436 MET cc_start: 0.9078 (ttm) cc_final: 0.8711 (tmm)
REVERT: A  550 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7749 (mtmt)
REVERT: A  640 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8292 (mp0)
REVERT: A  659 MET cc_start: 0.8038 (tpp) cc_final: 0.7581 (tpt)
REVERT: A  755 MET cc_start: 0.8082 (mtm) cc_final: 0.7767 (ptm)
REVERT: A  859 MET cc_start: 0.8999 (mmt) cc_final: 0.8754 (mmm)
REVERT: A  884 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8409 (tppt)
REVERT: A  925 ASP cc_start: 0.8623 (t0) cc_final: 0.8073 (t0)
REVERT: A  953 ASP cc_start: 0.8307 (t70) cc_final: 0.8081 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1756
  time to fit residues: 20.6113
Evaluate side-chains
  73 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0020
   chunk 81 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
A 590 GLN
A 635 GLN
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.073858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058898 restraints weight = 67108.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 6.56
r_work: 0.2858 rms_B_bonded: 6.30 restraints_weight: 2.0000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
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      :  0.002   0.033   7948  Z= 0.159
  Angle     :  0.589  11.066  10777  Z= 0.293
  Chirality :  0.042   0.203   1181
  Planarity :  0.005   0.048   1407
  Dihedral  :  4.549  41.229   1043
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.28 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.28), residues: 969
  helix:  1.25 (0.25), residues: 464
  sheet: -0.77 (0.41), residues: 163
  loop : -0.95 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 851 
 HIS   0.004   0.001   HIS A 186 
 PHE   0.029   0.001   PHE A 389 
 TYR   0.007   0.001   TYR A 450 
 ARG   0.004   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8386 (t0) cc_final: 0.7987 (t0)
REVERT: A  187 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7854 (mm-30)
REVERT: A  436 MET cc_start: 0.9147 (ttm) cc_final: 0.8739 (tmm)
REVERT: A  550 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7715 (mtmt)
REVERT: A  573 GLU cc_start: 0.7974 (pm20) cc_final: 0.7386 (pm20)
REVERT: A  640 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8286 (mp0)
REVERT: A  659 MET cc_start: 0.8057 (tpp) cc_final: 0.7505 (tpt)
REVERT: A  755 MET cc_start: 0.7903 (mtm) cc_final: 0.7698 (ptm)
REVERT: A  859 MET cc_start: 0.8984 (mmt) cc_final: 0.8749 (mmm)
REVERT: A  884 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8396 (tppt)
REVERT: A  925 ASP cc_start: 0.8672 (t0) cc_final: 0.7995 (t0)
REVERT: A  953 ASP cc_start: 0.8314 (t70) cc_final: 0.8099 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 79
  average time/residue: 0.1717
  time to fit residues: 19.7996
Evaluate side-chains
  67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 95 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 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 = 0.3362 r_free = 0.3362 target = 0.072355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.057664 restraints weight = 63865.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 6.30
r_work: 0.2829 rms_B_bonded: 6.12 restraints_weight: 2.0000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7948  Z= 0.209
  Angle     :  0.576   8.279  10777  Z= 0.292
  Chirality :  0.041   0.142   1181
  Planarity :  0.005   0.046   1407
  Dihedral  :  4.549  38.065   1043
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.21 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.29), residues: 969
  helix:  1.43 (0.25), residues: 459
  sheet: -0.60 (0.41), residues: 168
  loop : -0.85 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.025   0.001   PHE A 389 
 TYR   0.012   0.001   TYR A 388 
 ARG   0.004   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7945 (mm-30)
REVERT: A  436 MET cc_start: 0.9157 (ttm) cc_final: 0.8678 (tmm)
REVERT: A  573 GLU cc_start: 0.8181 (pm20) cc_final: 0.7623 (pm20)
REVERT: A  635 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8263 (pt0)
REVERT: A  640 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8293 (mp0)
REVERT: A  659 MET cc_start: 0.8114 (tpp) cc_final: 0.7513 (tpt)
REVERT: A  859 MET cc_start: 0.8981 (mmt) cc_final: 0.8764 (mmm)
REVERT: A  884 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8401 (tppt)
REVERT: A  925 ASP cc_start: 0.8653 (t0) cc_final: 0.8127 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1795
  time to fit residues: 17.7727
Evaluate side-chains
  69 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0060
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.9202

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 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 = 0.3351 r_free = 0.3351 target = 0.071778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057511 restraints weight = 52246.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 5.76
r_work: 0.2835 rms_B_bonded: 5.73 restraints_weight: 2.0000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7948  Z= 0.231
  Angle     :  0.581   7.751  10777  Z= 0.296
  Chirality :  0.042   0.147   1181
  Planarity :  0.005   0.045   1407
  Dihedral  :  4.617  42.016   1043
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.14 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 969
  helix:  1.42 (0.25), residues: 466
  sheet: -0.84 (0.40), residues: 178
  loop : -0.77 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 856 
 PHE   0.026   0.001   PHE A 389 
 TYR   0.013   0.002   TYR A 632 
 ARG   0.004   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7928 (mm-30)
REVERT: A  436 MET cc_start: 0.9170 (ttm) cc_final: 0.8686 (tmm)
REVERT: A  659 MET cc_start: 0.8138 (tpp) cc_final: 0.7770 (tpp)
REVERT: A  859 MET cc_start: 0.8997 (mmt) cc_final: 0.8791 (mmm)
REVERT: A  884 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8380 (tppt)
REVERT: A  925 ASP cc_start: 0.8699 (t0) cc_final: 0.8168 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2166
  time to fit residues: 21.3431
Evaluate side-chains
  67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 664 GLN
** A 987 GLN ** 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 = 0.3351 r_free = 0.3351 target = 0.071769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.057173 restraints weight = 62435.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 6.24
r_work: 0.2817 rms_B_bonded: 6.03 restraints_weight: 2.0000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7948  Z= 0.230
  Angle     :  0.589   7.706  10777  Z= 0.299
  Chirality :  0.042   0.144   1181
  Planarity :  0.005   0.045   1407
  Dihedral  :  4.645  43.581   1043
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.90 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.29), residues: 969
  helix:  1.47 (0.25), residues: 467
  sheet: -0.77 (0.39), residues: 179
  loop : -0.74 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 856 
 PHE   0.026   0.002   PHE A 389 
 TYR   0.012   0.001   TYR A 632 
 ARG   0.003   0.000   ARG A1037 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7946 (mm-30)
REVERT: A  436 MET cc_start: 0.9183 (ttm) cc_final: 0.8713 (tmm)
REVERT: A  659 MET cc_start: 0.8129 (tpp) cc_final: 0.7752 (tpp)
REVERT: A  680 MET cc_start: 0.8401 (ttt) cc_final: 0.8167 (ttt)
REVERT: A  859 MET cc_start: 0.9012 (mmt) cc_final: 0.8799 (mmm)
REVERT: A  884 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8428 (tppt)
REVERT: A  925 ASP cc_start: 0.8716 (t0) cc_final: 0.8199 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1819
  time to fit residues: 18.0022
Evaluate side-chains
  69 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** A 987 GLN ** 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 = 0.3312 r_free = 0.3312 target = 0.069890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055432 restraints weight = 65757.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 6.29
r_work: 0.2781 rms_B_bonded: 6.02 restraints_weight: 2.0000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7948  Z= 0.345
  Angle     :  0.650   7.412  10777  Z= 0.332
  Chirality :  0.044   0.154   1181
  Planarity :  0.005   0.045   1407
  Dihedral  :  4.935  45.921   1043
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.67 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.28), residues: 969
  helix:  1.17 (0.24), residues: 473
  sheet: -0.86 (0.39), residues: 178
  loop : -0.85 (0.38), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 851 
 HIS   0.005   0.001   HIS A 856 
 PHE   0.023   0.002   PHE A 389 
 TYR   0.016   0.002   TYR A 388 
 ARG   0.004   0.001   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: A  595 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8566 (mtp)
REVERT: A  659 MET cc_start: 0.8078 (tpp) cc_final: 0.7675 (tpp)
REVERT: A  884 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8439 (tppt)
REVERT: A  925 ASP cc_start: 0.8758 (t0) cc_final: 0.8227 (t0)
REVERT: B   20 PHE cc_start: 0.6232 (p90) cc_final: 0.5615 (p90)
  outliers start: 13
  outliers final: 9
  residues processed: 67
  average time/residue: 0.1762
  time to fit residues: 18.2235
Evaluate side-chains
  67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 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 = 0.3341 r_free = 0.3341 target = 0.072185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.058605 restraints weight = 41258.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 5.13
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7948  Z= 0.205
  Angle     :  0.599   8.430  10777  Z= 0.302
  Chirality :  0.041   0.142   1181
  Planarity :  0.004   0.046   1407
  Dihedral  :  4.665  42.681   1043
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.48 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.29), residues: 969
  helix:  1.44 (0.25), residues: 473
  sheet: -0.75 (0.40), residues: 176
  loop : -0.73 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 856 
 PHE   0.027   0.001   PHE A 389 
 TYR   0.011   0.001   TYR A 721 
 ARG   0.003   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7990 (mm-30)
REVERT: A  595 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8145 (mtp)
REVERT: A  659 MET cc_start: 0.7996 (tpp) cc_final: 0.7651 (tpp)
REVERT: A  884 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8294 (tppt)
REVERT: A  925 ASP cc_start: 0.8485 (t0) cc_final: 0.7987 (t0)
REVERT: B   20 PHE cc_start: 0.6030 (p90) cc_final: 0.5299 (p90)
  outliers start: 11
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1984
  time to fit residues: 18.7915
Evaluate side-chains
  68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  635 GLN
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.0570
   chunk 86 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0010
   chunk 40 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    0.6306

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN
** A 987 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.073869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.060044 restraints weight = 47334.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 5.47
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7948  Z= 0.162
  Angle     :  0.579   8.531  10777  Z= 0.291
  Chirality :  0.041   0.134   1181
  Planarity :  0.004   0.046   1407
  Dihedral  :  4.452  37.176   1043
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.95 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.29), residues: 969
  helix:  1.75 (0.25), residues: 463
  sheet: -0.59 (0.41), residues: 176
  loop : -0.56 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 851 
 HIS   0.012   0.001   HIS A 896 
 PHE   0.029   0.001   PHE A 389 
 TYR   0.009   0.001   TYR A 163 
 ARG   0.003   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7975 (mm-30)
REVERT: A  436 MET cc_start: 0.8643 (ttm) cc_final: 0.8312 (tmm)
REVERT: A  595 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (mtp)
REVERT: A  659 MET cc_start: 0.7981 (tpp) cc_final: 0.7681 (tpp)
REVERT: A  884 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8287 (tppt)
REVERT: A  925 ASP cc_start: 0.8450 (t0) cc_final: 0.7956 (t0)
REVERT: B   20 PHE cc_start: 0.6265 (p90) cc_final: 0.5460 (p90)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.2066
  time to fit residues: 19.8487
Evaluate side-chains
  64 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0050
   chunk 14 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 635 GLN
** A 987 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.073458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.059328 restraints weight = 51840.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 5.66
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7948  Z= 0.163
  Angle     :  0.592   9.266  10777  Z= 0.294
  Chirality :  0.040   0.134   1181
  Planarity :  0.004   0.043   1407
  Dihedral  :  4.450  34.902   1043
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.06 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.29), residues: 969
  helix:  1.80 (0.25), residues: 464
  sheet: -0.44 (0.40), residues: 176
  loop : -0.58 (0.38), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.029   0.001   PHE A 389 
 TYR   0.011   0.001   TYR A 721 
 ARG   0.004   0.000   ARG A 747 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4448.03 seconds
wall clock time: 78 minutes 49.35 seconds (4729.35 seconds total)