Starting phenix.real_space_refine
on Wed Jul 23 09:02:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yng_33961/07_2025/7yng_33961.cif"
  }
  resolution = 3.1
  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: 3
    Type Number    sf(0)   Gaussians
     C    1644      2.51       5
     N     456      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.71, per 1000 atoms: 0.65
  Number of scatterers: 2628
  At special positions: 0
  Unit cell: (115.54, 102.82, 31.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     528      8.00
     N     456      7.00
     C    1644      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: 0.57
  Conformation dependent library (CDL) restraints added in 340.4 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 50.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41
      removed outlier: 6.491A  pdb=" N   VAL A  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 58
      removed outlier: 8.372A  pdb=" N   GLU A  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   VAL B  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   HIS A  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   ALA B  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL A  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   VAL B  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   THR A  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   GLU B  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA A  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL F  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   HIS F  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66
      removed outlier: 6.350A  pdb=" N   GLN A  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ASN F  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   THR A  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.478A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82
      removed outlier: 6.841A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ALA B  78 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLN A  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B  80 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR A  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL A  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   VAL F  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ALA A  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   GLN F  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   ALA A  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 10.393A  pdb=" N   THR F  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   LYS A  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92
      removed outlier: 6.707A  pdb=" N   ALA A  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   THR F  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA A  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 40 through 41
      removed outlier: 6.490A  pdb=" N   VAL C  40 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58
      removed outlier: 6.840A  pdb=" N   VAL D  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL C  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   HIS D  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLY C  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   GLU C  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL E  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 10.429A  pdb=" N   GLY E  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   HIS C  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   ALA E  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL E  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   GLU E  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA C  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66
      removed outlier: 6.354A  pdb=" N   GLN C  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ASN D  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   THR C  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.478A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 82
      removed outlier: 6.283A  pdb=" N   VAL C  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   VAL D  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ALA C  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 10.068A  pdb=" N   GLN D  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   ALA C  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 10.393A  pdb=" N   THR D  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   LYS C  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL C  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ALA E  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLN C  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS E  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   THR C  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL E  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.708A  pdb=" N   ALA C  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   THR D  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA C  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    132 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: 0.56

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 462
        1.29 -     1.35: 408
        1.35 -     1.42: 108
        1.42 -     1.48: 450
        1.48 -     1.55: 1212
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" CA  SER D  87 "
       pdb=" C   SER D  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 2.00e+00
  bond pdb=" CA  SER A  87 "
       pdb=" C   SER A  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 2.00e+00
  bond pdb=" CA  SER F  87 "
       pdb=" C   SER F  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 1.91e+00
  bond pdb=" CA  SER E  87 "
       pdb=" C   SER E  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 1.89e+00
  bond pdb=" CA  SER B  87 "
       pdb=" C   SER B  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.510  0.018 1.35e-02 5.49e+03 1.83e+00
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 2914
        0.91 -     1.82: 472
        1.82 -     2.73: 130
        2.73 -     3.64: 36
        3.64 -     4.55: 18
  Bond angle restraints: 3570
  Sorted by residual:
  angle pdb=" C   THR A  92 "
        pdb=" N   GLY A  93 "
        pdb=" CA  GLY A  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.07   -3.08 1.13e+00 7.83e-01 7.42e+00
  angle pdb=" C   THR B  92 "
        pdb=" N   GLY B  93 "
        pdb=" CA  GLY B  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.05   -3.06 1.13e+00 7.83e-01 7.34e+00
  angle pdb=" C   THR D  92 "
        pdb=" N   GLY D  93 "
        pdb=" CA  GLY D  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.05   -3.06 1.13e+00 7.83e-01 7.33e+00
  angle pdb=" C   THR C  92 "
        pdb=" N   GLY C  93 "
        pdb=" CA  GLY C  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.04   -3.05 1.13e+00 7.83e-01 7.31e+00
  angle pdb=" C   THR F  92 "
        pdb=" N   GLY F  93 "
        pdb=" CA  GLY F  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.04   -3.05 1.13e+00 7.83e-01 7.28e+00
  ... (remaining 3565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 1368
       14.86 -    29.73: 138
       29.73 -    44.59: 36
       44.59 -    59.46: 0
       59.46 -    74.32: 6
  Dihedral angle restraints: 1548
    sinusoidal: 522
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" CA  GLY F  93 "
           pdb=" C   GLY F  93 "
           pdb=" N   PHE F  94 "
           pdb=" CA  PHE F  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLY A  93 "
           pdb=" C   GLY A  93 "
           pdb=" N   PHE A  94 "
           pdb=" CA  PHE A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLY D  93 "
           pdb=" C   GLY D  93 "
           pdb=" N   PHE D  94 "
           pdb=" CA  PHE D  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 1545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 156
       0.025 -    0.050: 144
       0.050 -    0.075: 68
       0.075 -    0.100: 59
       0.100 -    0.125: 41
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  VAL C  95 "
            pdb=" N   VAL C  95 "
            pdb=" C   VAL C  95 "
            pdb=" CB  VAL C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL E  95 "
            pdb=" N   VAL E  95 "
            pdb=" C   VAL E  95 "
            pdb=" CB  VAL E  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  VAL A  71 "
            pdb=" N   VAL A  71 "
            pdb=" C   VAL A  71 "
            pdb=" CB  VAL A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 465 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  83 "    0.005 2.00e-02 2.50e+03   1.01e-02 1.02e+00
        pdb=" C   GLU F  83 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   GLU F  83 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY F  84 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  83 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.01e+00
        pdb=" C   GLU B  83 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   GLU B  83 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY B  84 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  83 "   -0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   GLU C  83 "    0.017 2.00e-02 2.50e+03
        pdb=" O   GLU C  83 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY C  84 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 156
        2.73 -     3.28: 2535
        3.28 -     3.82: 4208
        3.82 -     4.36: 4429
        4.36 -     4.90: 9232
  Nonbonded interactions: 20560
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE1 GLN B  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS E  60 "
            pdb=" OE1 GLN E  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS A  60 "
            pdb=" OE1 GLN A  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS F  60 "
            pdb=" OE1 GLN F  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS C  60 "
            pdb=" OE1 GLN C  62 "
     model   vdw
     2.193 3.120
  ... (remaining 20555 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.180
  Find NCS groups from input model:        0.060
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
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      :  0.009   0.042   2640  Z= 0.415
  Angle     :  0.851   4.552   3570  Z= 0.495
  Chirality :  0.057   0.125    468
  Planarity :  0.003   0.010    444
  Dihedral  : 13.706  74.320    900
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -4.25 (0.31), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.23), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS D  50 
 PHE   0.011   0.004   PHE D  94 
 TYR   0.003   0.001   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18834 (   44)
  hydrogen bonds       : angle       7.21686 (  132)
  covalent geometry    : bond        0.00916 ( 2640)
  covalent geometry    : angle       0.85129 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8261 (mttt)
REVERT: F   45 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8415 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2710
  time to fit residues: 7.7564
Evaluate side-chains
  23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
D  79 GLN
F  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4993 r_free = 0.4993 target = 0.231832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.196690 restraints weight = 2584.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.4651 rms_B_bonded: 2.73
r_work: 0.4541 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2640  Z= 0.097
  Angle     :  0.470   4.163   3570  Z= 0.257
  Chirality :  0.052   0.131    468
  Planarity :  0.002   0.010    444
  Dihedral  :  4.485  14.411    378
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -3.06 (0.37), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.005   0.001   PHE F  94 
 TYR   0.004   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01582 (   44)
  hydrogen bonds       : angle       4.31228 (  132)
  covalent geometry    : bond        0.00217 ( 2640)
  covalent geometry    : angle       0.46980 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B   79 GLN cc_start: 0.8770 (tt0) cc_final: 0.8569 (tt0)
REVERT: F   45 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8258 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2617
  time to fit residues: 8.3800
Evaluate side-chains
  26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0970
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0040
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.8196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.224324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.187741 restraints weight = 2588.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 2.73
r_work: 0.4449 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2640  Z= 0.161
  Angle     :  0.478   3.584   3570  Z= 0.266
  Chirality :  0.051   0.124    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.569  13.828    378
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.73 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.008   0.002   PHE F  94 
 TYR   0.010   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01713 (   44)
  hydrogen bonds       : angle       4.01213 (  132)
  covalent geometry    : bond        0.00360 ( 2640)
  covalent geometry    : angle       0.47783 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.256 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8250 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2556
  time to fit residues: 6.4987
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0030
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.3396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.225093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.188346 restraints weight = 2605.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.4592 rms_B_bonded: 2.84
r_work: 0.4477 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2640  Z= 0.125
  Angle     :  0.432   3.110   3570  Z= 0.241
  Chirality :  0.051   0.124    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.246  12.410    378
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 10.00 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.47 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.007   0.002   PHE F  94 
 TYR   0.007   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01365 (   44)
  hydrogen bonds       : angle       3.72345 (  132)
  covalent geometry    : bond        0.00283 ( 2640)
  covalent geometry    : angle       0.43242 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.253 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8289 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 23
  average time/residue: 0.2312
  time to fit residues: 6.2090
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    0.0370
   chunk 2 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0170
   chunk 28 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.6102

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.224695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.187890 restraints weight = 2582.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.4565 rms_B_bonded: 2.80
r_work: 0.4450 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2640  Z= 0.141
  Angle     :  0.450   4.106   3570  Z= 0.251
  Chirality :  0.051   0.125    468
  Planarity :  0.002   0.007    444
  Dihedral  :  4.283  12.236    378
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 11.11 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.39 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS D  50 
 PHE   0.007   0.002   PHE F  94 
 TYR   0.008   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01452 (   44)
  hydrogen bonds       : angle       3.73151 (  132)
  covalent geometry    : bond        0.00318 ( 2640)
  covalent geometry    : angle       0.45038 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.233 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8282 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 21
  average time/residue: 0.1986
  time to fit residues: 4.9399
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0170
   overall best weight:    1.9224

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.220260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.183265 restraints weight = 2618.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4543 rms_B_bonded: 2.77
r_work: 0.4427 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2640  Z= 0.162
  Angle     :  0.468   4.483   3570  Z= 0.260
  Chirality :  0.051   0.126    468
  Planarity :  0.002   0.007    444
  Dihedral  :  4.412  12.989    378
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 11.48 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.38 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.007   0.002   PHE F  94 
 TYR   0.009   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01539 (   44)
  hydrogen bonds       : angle       3.77495 (  132)
  covalent geometry    : bond        0.00365 ( 2640)
  covalent geometry    : angle       0.46831 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.282 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8287 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 21
  average time/residue: 0.1940
  time to fit residues: 5.0034
Evaluate side-chains
  20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0980
   chunk 32 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0070
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.228565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.192355 restraints weight = 2651.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4638 rms_B_bonded: 2.81
r_work: 0.4526 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   2640  Z= 0.085
  Angle     :  0.415   5.474   3570  Z= 0.230
  Chirality :  0.050   0.124    468
  Planarity :  0.002   0.023    444
  Dihedral  :  3.817  10.962    378
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 12.59 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.18 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 
 PHE   0.005   0.001   PHE C  94 
 TYR   0.004   0.001   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01051 (   44)
  hydrogen bonds       : angle       3.45559 (  132)
  covalent geometry    : bond        0.00192 ( 2640)
  covalent geometry    : angle       0.41545 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.279 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8207 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 23
  average time/residue: 0.2239
  time to fit residues: 6.0882
Evaluate side-chains
  24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0670
   chunk 27 optimal weight:    0.0270
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0170
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.8218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.229041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.193270 restraints weight = 2546.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.4637 rms_B_bonded: 2.68
r_work: 0.4528 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.4395 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   2640  Z= 0.093
  Angle     :  0.416   5.020   3570  Z= 0.231
  Chirality :  0.050   0.124    468
  Planarity :  0.002   0.021    444
  Dihedral  :  3.670  10.128    378
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 12.96 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.08 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.57 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 PHE   0.006   0.002   PHE F  94 
 TYR   0.005   0.001   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01189 (   44)
  hydrogen bonds       : angle       3.39247 (  132)
  covalent geometry    : bond        0.00212 ( 2640)
  covalent geometry    : angle       0.41633 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.253 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8272 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.1971
  time to fit residues: 4.7646
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0670
   chunk 5 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.0124

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.229452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.193039 restraints weight = 2583.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 2.78
r_work: 0.4517 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.4383 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2640  Z= 0.101
  Angle     :  0.421   4.641   3570  Z= 0.233
  Chirality :  0.050   0.123    468
  Planarity :  0.002   0.018    444
  Dihedral  :  3.694  10.134    378
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 14.07 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.05 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS A  50 
 PHE   0.006   0.002   PHE F  94 
 TYR   0.005   0.001   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01280 (   44)
  hydrogen bonds       : angle       3.39194 (  132)
  covalent geometry    : bond        0.00231 ( 2640)
  covalent geometry    : angle       0.42089 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.281 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8264 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.2072
  time to fit residues: 5.0236
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0970
   chunk 28 optimal weight:    4.9990
   chunk 25 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    1.2780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.227430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.191195 restraints weight = 2577.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.4600 rms_B_bonded: 2.73
r_work: 0.4497 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.4361 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2640  Z= 0.119
  Angle     :  0.451   7.645   3570  Z= 0.249
  Chirality :  0.050   0.125    468
  Planarity :  0.002   0.017    444
  Dihedral  :  3.840  12.638    378
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 14.44 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.06 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.005   0.002   PHE C  94 
 TYR   0.006   0.001   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01385 (   44)
  hydrogen bonds       : angle       3.45844 (  132)
  covalent geometry    : bond        0.00271 ( 2640)
  covalent geometry    : angle       0.45097 ( 3570)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.267 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8270 (mttt)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.2372
  time to fit residues: 5.5827
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   79 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 23 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.4988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.223768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.187898 restraints weight = 2589.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.4580 rms_B_bonded: 2.66
r_work: 0.4473 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4338 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2640  Z= 0.134
  Angle     :  0.462   7.177   3570  Z= 0.255
  Chirality :  0.050   0.126    468
  Planarity :  0.002   0.016    444
  Dihedral  :  4.023  11.410    378
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 14.81 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -2.11 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.006   0.002   PHE C  94 
 TYR   0.007   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01502 (   44)
  hydrogen bonds       : angle       3.54589 (  132)
  covalent geometry    : bond        0.00306 ( 2640)
  covalent geometry    : angle       0.46206 ( 3570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1779.91 seconds
wall clock time: 31 minutes 20.84 seconds (1880.84 seconds total)