Starting phenix.real_space_refine
on Thu Sep 10 21:34:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7efc_31083/09_2026/7efc_31083.map"
  }
  resolution = 1.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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       4      5.16       5
     C    2392      2.51       5
     N     668      2.21       5
     O     940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4004
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 946
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 896
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 1, 'TRANS': 118}
      Conformer: "B"
        Number of residues, atoms: 120, 896
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 1, 'TRANS': 118}
          bond proxies already assigned to first conformer: 867
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 40, 55
          Unusual residues: {'BTN': 1}
          Classifications: {'undetermined': 1, 'water': 39}
          Link IDs: {None: 39}
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}
  Restraints were copied for chains:
    B, C, D
  Residues with excluded nonbonded symmetry interactions: 56
    residue:
      pdb=" N  ASER A  45 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  45 " occ=0.50
    residue:
      pdb=" N  AALA A  46 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A  46 " occ=0.50
    residue:
      pdb=" N  AVAL A  47 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL A  47 " occ=0.50
    residue:
      pdb=" N  AGLY A  48 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A  48 " occ=0.50
    residue:
      pdb=" N  AASN A  49 " occ=0.50
      ... (14 atoms not shown)
      pdb=" ND2BASN A  49 " occ=0.50
    residue:
      pdb=" N  AALA A  50 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A  50 " occ=0.50
    residue:
      pdb=" N  AGLU A  51 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A  51 " occ=0.50
    residue:
      pdb=" N  ASER A  52 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  52 " occ=0.50
    residue:
      pdb=" C10ABTN A5100 " occ=0.50
      ... (14 atoms not shown)
      pdb=" S1 ABTN A5100 " occ=0.50
    residue:
      pdb=" O  AHOH A5221 " occ=0.50
    residue:
      pdb=" O   HOH A5223 " occ=0.50
    residue:
      pdb=" O  AHOH A5231 " occ=0.50
    ... (remaining 44 not shown)
  Time building chain proxies: 1.00, per 1000 atoms: 0.25
  Number of scatterers: 4004
  At special positions: 0
  Unit cell: (68.8516, 64.4096, 58.4869, 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       4     16.00
     O     940      8.00
     N     668      7.00
     C    2392      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: 0.30
  Conformation dependent library (CDL) restraints added in 211.3 milliseconds
  

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 4 sheets defined
      3.3% alpha, 53.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'D' and resid 118 through 121
    Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG A  53 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS A  80 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL A  55 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA A  78 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR A  71 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY A  94 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU A  73 " --> pdb=" O   TRP A  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP A  92 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP A  75 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR A  90 " --> pdb=" O   TRP A  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL A  77 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER A  88 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP A  79 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG B  53 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS B  80 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL B  55 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA B  78 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR B  71 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY B  94 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU B  73 " --> pdb=" O   TRP B  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP B  92 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP B  75 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR B  90 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL B  77 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER B  88 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP B  79 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG C  53 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS C  80 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL C  55 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA C  78 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR C  71 " --> pdb=" O   GLY C  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY C  94 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU C  73 " --> pdb=" O   TRP C  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP C  92 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP C  75 " --> pdb=" O   THR C  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR C  90 " --> pdb=" O   TRP C  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL C  77 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER C  88 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP C  79 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23
      removed outlier: 8.184A  pdb=" N   ARG D  53 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS D  80 " --> pdb=" O   ARG D  53 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL D  55 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA D  78 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   THR D  71 " --> pdb=" O   GLY D  94 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY D  94 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU D  73 " --> pdb=" O   TRP D  92 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP D  92 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   TRP D  75 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR D  90 " --> pdb=" O   TRP D  75 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL D  77 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER D  88 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TRP D  79 " --> pdb=" O   ALA D  86 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    456 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: 0.64

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 548
        1.29 -     1.42: 880
        1.42 -     1.55: 2192
        1.55 -     1.68: 316
        1.68 -     1.81: 8
  Bond restraints: 3944
  Sorted by residual:
  bond pdb=" C   GLY C  94 "
       pdb=" O   GLY C  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY D  94 "
       pdb=" O   GLY D  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY B  94 "
       pdb=" O   GLY B  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   GLY A  94 "
       pdb=" O   GLY A  94 "
    ideal  model  delta    sigma   weight residual
    1.232  1.307 -0.075 1.05e-02 9.07e+03 5.12e+01
  bond pdb=" C   ILE C  17 "
       pdb=" O   ILE C  17 "
    ideal  model  delta    sigma   weight residual
    1.237  1.154  0.083 1.19e-02 7.06e+03 4.86e+01
  ... (remaining 3939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 3396
        2.66 -     5.33: 1508
        5.33 -     7.99: 428
        7.99 -    10.65: 44
       10.65 -    13.32: 24
  Bond angle restraints: 5400
  Sorted by residual:
  angle pdb=" CA  PHE D  29 "
        pdb=" CB  PHE D  29 "
        pdb=" CG  PHE D  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE B  29 "
        pdb=" CB  PHE B  29 "
        pdb=" CG  PHE B  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE A  29 "
        pdb=" CB  PHE A  29 "
        pdb=" CG  PHE A  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  PHE C  29 "
        pdb=" CB  PHE C  29 "
        pdb=" CG  PHE C  29 "
      ideal   model   delta    sigma   weight residual
     113.80  124.22  -10.42 1.00e+00 1.00e+00 1.08e+02
  angle pdb=" CA  ILE A  17 "
        pdb=" C   ILE A  17 "
        pdb=" O   ILE A  17 "
      ideal   model   delta    sigma   weight residual
     120.85  110.38   10.47 1.06e+00 8.90e-01 9.75e+01
  ... (remaining 5395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 1952
       16.54 -    33.08: 156
       33.08 -    49.62: 20
       49.62 -    66.16: 12
       66.16 -    82.70: 12
  Dihedral angle restraints: 2152
    sinusoidal: 728
      harmonic: 1424
  Sorted by residual:
  dihedral pdb=" CA ASER B  52 "
           pdb=" C  ASER B  52 "
           pdb=" N   ARG B  53 "
           pdb=" CA  ARG B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA ASER D  52 "
           pdb=" C  ASER D  52 "
           pdb=" N   ARG D  53 "
           pdb=" CA  ARG D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA ASER A  52 "
           pdb=" C  ASER A  52 "
           pdb=" N   ARG A  53 "
           pdb=" CA  ARG A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.36  -28.64     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 2149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 412
       0.080 -    0.160: 164
       0.160 -    0.241: 20
       0.241 -    0.321: 0
       0.321 -    0.401: 8
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CB  VAL A  31 "
            pdb=" CA  VAL A  31 "
            pdb=" CG1 VAL A  31 "
            pdb=" CG2 VAL A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  chirality pdb=" CB  VAL C  31 "
            pdb=" CA  VAL C  31 "
            pdb=" CG1 VAL C  31 "
            pdb=" CG2 VAL C  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  chirality pdb=" CB  VAL B  31 "
            pdb=" CA  VAL B  31 "
            pdb=" CG1 VAL B  31 "
            pdb=" CG2 VAL B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.02e+00
  ... (remaining 601 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN C5100 "   -0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN C5100 "    0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN C5100 "    0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN C5100 "   -0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN C5100 "   -0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN C5100 "    0.262 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN A5100 "   -0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN A5100 "    0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN A5100 "    0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN A5100 "   -0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN A5100 "   -0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN A5100 "    0.262 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3 ABTN B5100 "    0.063 2.00e-02 2.50e+03   2.15e-01 6.96e+02
        pdb=" C4 ABTN B5100 "   -0.172 2.00e-02 2.50e+03
        pdb=" C5 ABTN B5100 "   -0.172 2.00e-02 2.50e+03
        pdb=" N1 ABTN B5100 "    0.270 2.00e-02 2.50e+03
        pdb=" N2 ABTN B5100 "    0.272 2.00e-02 2.50e+03
        pdb=" O3 ABTN B5100 "   -0.262 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        0.00 -     0.98: 2
        0.98 -     1.96: 0
        1.96 -     2.94: 1438
        2.94 -     3.92: 11594
        3.92 -     4.90: 22880
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 35914
  Sorted by model distance:
  nonbonded pdb=" O   HOH A5223 "
            pdb=" O   HOH C5223 "
     model   vdw
     0.001 3.040
  nonbonded pdb=" O   HOH B5223 "
            pdb=" O   HOH D5223 "
     model   vdw
     0.001 3.040
  nonbonded pdb=" O  AASN C  49 "
            pdb=" OD1AASN C  49 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O  AASN D  49 "
            pdb=" OD1AASN D  49 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" O  AASN A  49 "
            pdb=" OD1AASN A  49 "
     model   vdw
     2.057 3.040
  ... (remaining 35909 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.94
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:             0.220
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.032   0.090   3944  Z= 2.144
  Angle     :  3.162  13.316   5400  Z= 2.201
  Chirality :  0.090   0.401    604
  Planarity :  0.016   0.215    684
  Dihedral  : 15.028  82.705   1264
  Min Nonbonded Distance : 0.001

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  2.54 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  4.30 %
    Favored  : 93.55 %
  Cbeta Deviations :  3.60 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.33), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.30 (0.29), residues: 244
  loop : -1.41 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  53 
 TYR   0.002   0.001   TYR B  60 
 PHE   0.002   0.001   PHE D 130 
 TRP   0.004   0.001   TRP C  92 
 HIS   0.001   0.000   HIS C 127 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.03226 /  2.14 ( 3944)
  covalent geometry    : angle       3.16201 /  2.20 ( 5400)
  hydrogen bonds       : bond        0.13857 /  9.04 (  168)
  hydrogen bonds       : angle       9.73459 /  6.77 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.8217 (m) cc_final: 0.7789 (p)
REVERT: A   53 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7498 (ttp80)
REVERT: A   69 SER cc_start: 0.7845 (m) cc_final: 0.7634 (t)
REVERT: A  103 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7435 (mtm-85)
REVERT: B   27 SER cc_start: 0.8218 (m) cc_final: 0.7790 (p)
REVERT: B   53 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7499 (ttp80)
REVERT: B   69 SER cc_start: 0.7845 (m) cc_final: 0.7635 (t)
REVERT: B  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7434 (mtm-85)
REVERT: C   27 SER cc_start: 0.8215 (m) cc_final: 0.7788 (p)
REVERT: C   53 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7498 (ttp80)
REVERT: C   69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t)
REVERT: C  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7433 (mtm-85)
REVERT: D   27 SER cc_start: 0.8217 (m) cc_final: 0.7788 (p)
REVERT: D   53 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7500 (ttp80)
REVERT: D   69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t)
REVERT: D  103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7435 (mtm-85)
  outliers start: 4
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5104
  time to fit residues: 33.8894
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.1990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.162592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.137983 restraints weight = 4542.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 1.31
r_work: 0.3672 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3565 r_free = 0.3565    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (13 function evaluations)
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3944  Z= 0.191
  Angle     :  0.751   7.083   5400  Z= 0.419
  Chirality :  0.045   0.137    604
  Planarity :  0.004   0.037    684
  Dihedral  :  8.267  49.241    576
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  1.69 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  3.23 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.37), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.42 (0.24), residues: 300
  loop :  0.65 (0.52), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  53 
 TYR   0.011   0.002   TYR B  22 
 PHE   0.025   0.004   PHE C  29 
 TRP   0.014   0.003   TRP D  92 
 HIS   0.004   0.002   HIS B  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 3944)
  covalent geometry    : angle       0.75092 /  0.42 ( 5400)
  hydrogen bonds       : bond        0.05146 /  3.60 (  168)
  hydrogen bonds       : angle       8.02390 /  5.66 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7424 (ttm110)
REVERT: B   53 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7424 (ttm110)
REVERT: C   53 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7421 (ttm110)
REVERT: D   53 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7419 (ttm110)
  outliers start: 4
  outliers final: 0
  residues processed: 68
  average time/residue: 0.5183
  time to fit residues: 36.4999
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    3.7388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.162408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.139005 restraints weight = 3639.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 1.17
r_work: 0.3672 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3567 r_free = 0.3567    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3944  Z= 0.201
  Angle     :  0.703   6.172   5400  Z= 0.390
  Chirality :  0.046   0.148    604
  Planarity :  0.004   0.027    684
  Dihedral  :  7.717  39.396    572
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  2.54 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.60 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.37), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.43 (0.24), residues: 296
  loop :  1.20 (0.51), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.002   ARG A  53 
 TYR   0.016   0.003   TYR B  22 
 PHE   0.022   0.004   PHE C  29 
 TRP   0.013   0.003   TRP D  92 
 HIS   0.004   0.002   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.20 ( 3944)
  covalent geometry    : angle       0.70332 /  0.39 ( 5400)
  hydrogen bonds       : bond        0.05203 /  3.57 (  168)
  hydrogen bonds       : angle       7.79991 /  5.47 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7519 (ttp80)
REVERT: B   53 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7515 (ttp80)
REVERT: C   53 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7515 (ttp80)
REVERT: D   53 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7507 (ttp80)
  outliers start: 4
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5934
  time to fit residues: 34.2607
Evaluate side-chains
  56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    0.0000
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.7790

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.162113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.137458 restraints weight = 4350.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.30
r_work: 0.3662 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3559 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3944  Z= 0.203
  Angle     :  0.688   6.168   5400  Z= 0.379
  Chirality :  0.045   0.149    604
  Planarity :  0.004   0.023    684
  Dihedral  :  7.753  38.559    572
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.68 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.36), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.41 (0.25), residues: 296
  loop :  1.14 (0.50), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.002   ARG A  53 
 TYR   0.007   0.002   TYR D  96 
 PHE   0.016   0.003   PHE D  29 
 TRP   0.013   0.003   TRP A  92 
 HIS   0.004   0.002   HIS C  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.20 ( 3944)
  covalent geometry    : angle       0.68840 /  0.38 ( 5400)
  hydrogen bonds       : bond        0.05181 /  3.53 (  168)
  hydrogen bonds       : angle       7.84735 /  5.49 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7672 (ttp80)
REVERT: C   53 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7676 (ttp80)
REVERT: D   53 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7664 (ttp80)
  outliers start: 8
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5853
  time to fit residues: 33.8620
Evaluate side-chains
  56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain D residue   28 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    5.1990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.161715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137431 restraints weight = 4367.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.29
r_work: 0.3657 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3944  Z= 0.257
  Angle     :  0.719   4.326   5400  Z= 0.402
  Chirality :  0.046   0.146    604
  Planarity :  0.005   0.027    684
  Dihedral  :  8.050  38.084    572
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.36), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.35 (0.25), residues: 296
  loop :  0.79 (0.49), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.002   ARG C  84 
 TYR   0.008   0.002   TYR B  60 
 PHE   0.010   0.003   PHE A  29 
 TRP   0.014   0.004   TRP C  92 
 HIS   0.005   0.003   HIS B  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.26 ( 3944)
  covalent geometry    : angle       0.71874 /  0.40 ( 5400)
  hydrogen bonds       : bond        0.05575 /  3.78 (  168)
  hydrogen bonds       : angle       8.10952 /  5.66 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.6503
  time to fit residues: 34.8116
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 41 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    2.4788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.163256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.138666 restraints weight = 4741.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 1.35
r_work: 0.3669 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3944  Z= 0.154
  Angle     :  0.625   4.849   5400  Z= 0.342
  Chirality :  0.044   0.148    604
  Planarity :  0.003   0.019    684
  Dihedral  :  7.330  36.154    572
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.83 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.33), residues: 512
  helix: -5.19 (0.15), residues: 24
  sheet:  0.47 (0.25), residues: 296
  loop : -0.17 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 103 
 TYR   0.006   0.001   TYR D  96 
 PHE   0.007   0.002   PHE B  29 
 TRP   0.011   0.002   TRP D 108 
 HIS   0.003   0.002   HIS D  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.15 ( 3944)
  covalent geometry    : angle       0.62549 /  0.34 ( 5400)
  hydrogen bonds       : bond        0.04944 /  3.39 (  168)
  hydrogen bonds       : angle       7.72002 /  5.40 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.8184 (m) cc_final: 0.7973 (p)
REVERT: A  103 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7556 (ttm110)
REVERT: B   27 SER cc_start: 0.8178 (m) cc_final: 0.7966 (p)
REVERT: B  103 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7564 (ttm110)
REVERT: C   27 SER cc_start: 0.8179 (m) cc_final: 0.7968 (p)
REVERT: C  103 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7556 (ttm110)
REVERT: D   27 SER cc_start: 0.8180 (m) cc_final: 0.7966 (p)
REVERT: D  103 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7557 (ttm110)
  outliers start: 4
  outliers final: 0
  residues processed: 48
  average time/residue: 0.6241
  time to fit residues: 30.9073
Evaluate side-chains
  52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain D residue  103 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.4980
   chunk 33 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    3.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  82 ASN
C  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.162505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138231 restraints weight = 4432.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.30
r_work: 0.3665 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3944  Z= 0.193
  Angle     :  0.670   5.048   5400  Z= 0.366
  Chirality :  0.045   0.152    604
  Planarity :  0.004   0.024    684
  Dihedral  :  7.703  36.657    572
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  9.68 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.33), residues: 512
  helix: -5.19 (0.15), residues: 24
  sheet:  0.42 (0.25), residues: 296
  loop : -0.29 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  84 
 TYR   0.007   0.002   TYR C  96 
 PHE   0.010   0.003   PHE D  29 
 TRP   0.012   0.003   TRP D  92 
 HIS   0.004   0.002   HIS C  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 3944)
  covalent geometry    : angle       0.67046 /  0.37 ( 5400)
  hydrogen bonds       : bond        0.05124 /  3.49 (  168)
  hydrogen bonds       : angle       7.86394 /  5.49 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7559 (ttm110)
REVERT: B  103 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7571 (ttm110)
REVERT: C  103 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7564 (ttm110)
REVERT: D  103 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7563 (ttm110)
  outliers start: 12
  outliers final: 8
  residues processed: 52
  average time/residue: 0.5793
  time to fit residues: 31.1754
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue  103 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.161841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.138297 restraints weight = 3996.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 1.23
r_work: 0.3664 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3944  Z= 0.234
  Angle     :  0.716   6.106   5400  Z= 0.390
  Chirality :  0.047   0.157    604
  Planarity :  0.004   0.030    684
  Dihedral  :  7.916  36.860    572
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  9.68 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.35), residues: 512
  helix:  None (None), residues: 0
  sheet:  0.35 (0.25), residues: 296
  loop :  0.49 (0.47), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.002   ARG D  84 
 TYR   0.007   0.002   TYR C  96 
 PHE   0.007   0.002   PHE D  29 
 TRP   0.014   0.003   TRP A  92 
 HIS   0.005   0.003   HIS A  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.23 ( 3944)
  covalent geometry    : angle       0.71631 /  0.39 ( 5400)
  hydrogen bonds       : bond        0.05461 /  3.71 (  168)
  hydrogen bonds       : angle       7.88458 /  5.49 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7534 (ttm110)
REVERT: B  103 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7539 (ttm110)
REVERT: C  103 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7539 (ttm110)
REVERT: D  103 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7534 (ttm110)
  outliers start: 12
  outliers final: 8
  residues processed: 52
  average time/residue: 0.6393
  time to fit residues: 34.3716
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue  103 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   overall best weight:    3.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  82 ASN
D  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.162382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138424 restraints weight = 4140.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 1.26
r_work: 0.3667 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (12 function evaluations)
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3944  Z= 0.179
  Angle     :  0.672   7.427   5400  Z= 0.359
  Chirality :  0.045   0.156    604
  Planarity :  0.004   0.023    684
  Dihedral  :  7.546  38.706    572
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  9.68 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.33), residues: 512
  helix: -5.20 (0.15), residues: 24
  sheet:  0.45 (0.25), residues: 296
  loop : -0.53 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  59 
 TYR   0.006   0.002   TYR C  96 
 PHE   0.005   0.002   PHE B  29 
 TRP   0.012   0.003   TRP C  92 
 HIS   0.003   0.002   HIS C  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.18 ( 3944)
  covalent geometry    : angle       0.67209 /  0.36 ( 5400)
  hydrogen bonds       : bond        0.05093 /  3.51 (  168)
  hydrogen bonds       : angle       7.62640 /  5.31 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 SER cc_start: 0.8192 (m) cc_final: 0.7947 (p)
REVERT: A  103 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7517 (ttm110)
REVERT: B   27 SER cc_start: 0.8188 (m) cc_final: 0.7941 (p)
REVERT: B  103 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7522 (ttm110)
REVERT: C   27 SER cc_start: 0.8189 (m) cc_final: 0.7948 (p)
REVERT: C  103 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7538 (ttm110)
REVERT: D   27 SER cc_start: 0.8185 (m) cc_final: 0.7936 (p)
REVERT: D  103 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7530 (ttm110)
  outliers start: 12
  outliers final: 8
  residues processed: 52
  average time/residue: 0.5875
  time to fit residues: 31.5897
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue  103 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.9502

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.163408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.139057 restraints weight = 4405.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.32
r_work: 0.3675 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3944  Z= 0.136
  Angle     :  0.637   7.688   5400  Z= 0.333
  Chirality :  0.044   0.159    604
  Planarity :  0.003   0.015    684
  Dihedral  :  7.094  39.364    572
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  :  9.68 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.33), residues: 512
  helix: -5.20 (0.16), residues: 24
  sheet:  0.51 (0.25), residues: 296
  loop : -0.46 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 103 
 TYR   0.005   0.001   TYR D  96 
 PHE   0.004   0.002   PHE C  29 
 TRP   0.011   0.002   TRP C 108 
 HIS   0.002   0.001   HIS D  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 ( 3944)
  covalent geometry    : angle       0.63714 /  0.33 ( 5400)
  hydrogen bonds       : bond        0.04765 /  3.33 (  168)
  hydrogen bonds       : angle       7.36700 /  5.15 (  456)

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

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

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1024 Ramachandran restraints generated.
    512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7531 (ttm110)
REVERT: B  103 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7535 (ttm110)
REVERT: C  103 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7550 (ttm110)
REVERT: D  103 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7544 (ttm110)
  outliers start: 12
  outliers final: 8
  residues processed: 52
  average time/residue: 0.5984
  time to fit residues: 32.2428
Evaluate side-chains
  56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   69 SER
Chi-restraints excluded: chain B residue  103 ARG
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain D residue  103 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.0770
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    0.4980
   overall best weight:    2.2542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  82 ASN
D  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.163400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138502 restraints weight = 4985.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 1.38
r_work: 0.3664 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3944  Z= 0.147
  Angle     :  0.631   6.115   5400  Z= 0.335
  Chirality :  0.044   0.156    604
  Planarity :  0.003   0.018    684
  Dihedral  :  7.197  39.461    572
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 10.75 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.33), residues: 512
  helix: -5.21 (0.15), residues: 24
  sheet:  0.54 (0.25), residues: 296
  loop : -0.39 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.006   0.001   TYR C  96 
 PHE   0.005   0.002   PHE B  29 
 TRP   0.011   0.002   TRP C 108 
 HIS   0.002   0.001   HIS C  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.15 ( 3944)
  covalent geometry    : angle       0.63124 /  0.34 ( 5400)
  hydrogen bonds       : bond        0.04881 /  3.41 (  168)
  hydrogen bonds       : angle       7.39527 /  5.17 (  456)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2290.92 seconds
wall clock time: 39 minutes 56.41 seconds (2396.41 seconds total)