Starting phenix.real_space_refine
on Fri Aug 22 14:05:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oqi_17111/08_2025/8oqi_17111.map"
  }
  resolution = 3.1
  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=   0.012
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    2370      2.51       5
     N     660      2.21       5
     O     780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3810
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 381
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.49, per 1000 atoms: 0.13
  Number of scatterers: 3810
  At special positions: 0
  Unit cell: (90.1, 90.1, 41.34, 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     780      8.00
     N     660      7.00
     C    2370      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: 0.27
  Conformation dependent library (CDL) restraints added in 117.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50
      removed outlier: 6.834A  pdb=" N   VAL A  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL C  49 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS A  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL C  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL E  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS C  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL E  48 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL G  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS E  50 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL G  48 " --> pdb=" O   GLY I  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL I  49 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS G  50 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57
      removed outlier: 6.463A  pdb=" N   THR A  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   GLU C  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA A  56 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU E  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA C  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR E  54 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU G  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA E  56 " --> pdb=" O   GLU G  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR G  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU I  57 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ALA G  56 " --> pdb=" O   GLU I  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66
      removed outlier: 6.410A  pdb=" N   ASN A  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN C  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN E  65 " --> pdb=" O   VAL G  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN G  65 " --> pdb=" O   VAL I  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 72
      removed outlier: 6.364A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL E  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL G  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81
      removed outlier: 6.638A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   THR C  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS A  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   THR E  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS C  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA E  78 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   THR G  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LYS E  80 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA G  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 8.469A  pdb=" N   THR I  81 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS G  80 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88
      removed outlier: 6.278A  pdb=" N   SER A  87 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER C  87 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER E  87 " --> pdb=" O   ILE G  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER G  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50
      removed outlier: 6.834A  pdb=" N   VAL B  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL D  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS B  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL D  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL F  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS D  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL F  48 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL H  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS F  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL H  48 " --> pdb=" O   GLY J  47 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   VAL J  49 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS H  50 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 57
      removed outlier: 6.463A  pdb=" N   THR B  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU D  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA B  56 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR D  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU F  57 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA D  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR F  54 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU H  57 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA F  56 " --> pdb=" O   GLU H  57 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR H  54 " --> pdb=" O   VAL J  55 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU J  57 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA H  56 " --> pdb=" O   GLU J  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66
      removed outlier: 6.410A  pdb=" N   ASN B  65 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN D  65 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN F  65 " --> pdb=" O   VAL H  66 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASN H  65 " --> pdb=" O   VAL J  66 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 72
      removed outlier: 6.364A  pdb=" N   VAL B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL F  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL H  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 78 through 81
      removed outlier: 6.638A  pdb=" N   ALA B  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   THR D  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS B  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA D  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 8.469A  pdb=" N   THR F  81 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS D  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ALA F  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 8.469A  pdb=" N   THR H  81 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LYS F  80 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA H  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   THR J  81 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LYS H  80 " --> pdb=" O   THR J  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 88
      removed outlier: 6.278A  pdb=" N   SER B  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER D  87 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER F  87 " --> pdb=" O   ILE H  88 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER H  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 92

    24 hydrogen bonds defined for protein.
    72 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: 0.49

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 670
        1.28 -     1.35: 610
        1.35 -     1.41: 150
        1.41 -     1.48: 205
        1.48 -     1.54: 2195
  Bond restraints: 3830
  Sorted by residual:
  bond pdb=" N   VAL E  63 "
       pdb=" CA  VAL E  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.035 1.14e-02 7.69e+03 9.67e+00
  bond pdb=" N   VAL D  63 "
       pdb=" CA  VAL D  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.035 1.14e-02 7.69e+03 9.65e+00
  bond pdb=" N   VAL B  49 "
       pdb=" CA  VAL B  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.52e+00
  bond pdb=" N   VAL A  63 "
       pdb=" CA  VAL A  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.035 1.14e-02 7.69e+03 9.52e+00
  bond pdb=" N   VAL J  74 "
       pdb=" CA  VAL J  74 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.19e-02 7.06e+03 9.50e+00
  ... (remaining 3825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 2450
        1.12 -     2.25: 1223
        2.25 -     3.37: 964
        3.37 -     4.49: 431
        4.49 -     5.62: 122
  Bond angle restraints: 5190
  Sorted by residual:
  angle pdb=" CA  HIS H  50 "
        pdb=" CB  HIS H  50 "
        pdb=" CG  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     113.80  118.77   -4.97 1.00e+00 1.00e+00 2.47e+01
  angle pdb=" CA  HIS C  50 "
        pdb=" CB  HIS C  50 "
        pdb=" CG  HIS C  50 "
      ideal   model   delta    sigma   weight residual
     113.80  118.77   -4.97 1.00e+00 1.00e+00 2.47e+01
  angle pdb=" CA  HIS A  50 "
        pdb=" CB  HIS A  50 "
        pdb=" CG  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     113.80  118.77   -4.97 1.00e+00 1.00e+00 2.47e+01
  angle pdb=" CA  HIS E  50 "
        pdb=" CB  HIS E  50 "
        pdb=" CG  HIS E  50 "
      ideal   model   delta    sigma   weight residual
     113.80  118.77   -4.97 1.00e+00 1.00e+00 2.47e+01
  angle pdb=" CA  HIS I  50 "
        pdb=" CB  HIS I  50 "
        pdb=" CG  HIS I  50 "
      ideal   model   delta    sigma   weight residual
     113.80  118.76   -4.96 1.00e+00 1.00e+00 2.46e+01
  ... (remaining 5185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.11 -    14.89: 1870
       14.89 -    29.66: 220
       29.66 -    44.43: 60
       44.43 -    59.20: 30
       59.20 -    73.97: 20
  Dihedral angle restraints: 2200
    sinusoidal: 700
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  GLU H  83 "
           pdb=" CB  GLU H  83 "
           pdb=" CG  GLU H  83 "
           pdb=" CD  GLU H  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.94  -55.06     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CA  GLU I  83 "
           pdb=" CB  GLU I  83 "
           pdb=" CG  GLU I  83 "
           pdb=" CD  GLU I  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.94  -55.06     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CA  GLU C  83 "
           pdb=" CB  GLU C  83 "
           pdb=" CG  GLU C  83 "
           pdb=" CD  GLU C  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.95  -55.05     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 2197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.045: 100
       0.045 -    0.087: 180
       0.087 -    0.129: 220
       0.129 -    0.171: 90
       0.171 -    0.213: 90
  Chirality restraints: 680
  Sorted by residual:
  chirality pdb=" CA  LYS D  45 "
            pdb=" N   LYS D  45 "
            pdb=" C   LYS D  45 "
            pdb=" CB  LYS D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  HIS I  50 "
            pdb=" N   HIS I  50 "
            pdb=" C   HIS I  50 "
            pdb=" CB  HIS I  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  LYS C  45 "
            pdb=" N   LYS C  45 "
            pdb=" C   LYS C  45 "
            pdb=" CB  LYS C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 677 not shown)

  Planarity restraints: 650
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  64 "   -0.010 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   THR E  64 "    0.037 2.00e-02 2.50e+03
        pdb=" O   THR E  64 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN E  65 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H  64 "    0.010 2.00e-02 2.50e+03   2.16e-02 4.64e+00
        pdb=" C   THR H  64 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR H  64 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASN H  65 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G  64 "   -0.010 2.00e-02 2.50e+03   2.15e-02 4.60e+00
        pdb=" C   THR G  64 "    0.037 2.00e-02 2.50e+03
        pdb=" O   THR G  64 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN G  65 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 647 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 1772
        2.95 -     3.44: 3537
        3.44 -     3.93: 6175
        3.93 -     4.41: 6924
        4.41 -     4.90: 13698
  Nonbonded interactions: 32106
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN G  65 "
            pdb=" O   GLY G  68 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" ND2 ASN D  65 "
            pdb=" O   GLY D  68 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" ND2 ASN C  65 "
            pdb=" O   GLY C  68 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" ND2 ASN B  65 "
            pdb=" O   GLY B  68 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" ND2 ASN J  65 "
            pdb=" O   GLY J  68 "
     model   vdw
     2.465 3.120
  ... (remaining 32101 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.130
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.470
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
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      :  0.013   0.039   3830  Z= 0.988
  Angle     :  2.008   5.618   5190  Z= 1.508
  Chirality :  0.115   0.213    680
  Planarity :  0.007   0.022    650
  Dihedral  : 18.286  73.975   1260
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.42 %
    Favored  : 78.95 %
  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 aren not related in a simple way.
  whole:  0.22 (0.36), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.18 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR J  39 
 PHE   0.002   0.001   PHE G  94 
 HIS   0.011   0.007   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01311 ( 3830)
  covalent geometry    : angle       2.00804 ( 5190)
  hydrogen bonds       : bond        0.16975 (   24)
  hydrogen bonds       : angle       8.70612 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.102 
Fit side-chains
REVERT: C   80 LYS cc_start: 0.9030 (tttp) cc_final: 0.8598 (tttm)
REVERT: D   60 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7510 (mttp)
REVERT: E   60 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7582 (mttp)
REVERT: E   80 LYS cc_start: 0.9021 (tttp) cc_final: 0.8763 (tttp)
REVERT: H   60 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7436 (mttt)
  outliers start: 10
  outliers final: 2
  residues processed: 88
  average time/residue: 0.0789
  time to fit residues: 8.3158
Evaluate side-chains
  80 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain I residue   81 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.133722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.116523 restraints weight = 5001.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.32
r_work: 0.3533 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   3830  Z= 0.105
  Angle     :  0.436   2.600   5190  Z= 0.269
  Chirality :  0.051   0.117    680
  Planarity :  0.002   0.009    650
  Dihedral  :  5.577  43.458    562
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.42 %
    Favored  : 78.95 %
  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 aren not related in a simple way.
  whole: -0.51 (0.36), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.38 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR B  39 
 PHE   0.010   0.002   PHE E  94 
 HIS   0.003   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 3830)
  covalent geometry    : angle       0.43612 ( 5190)
  hydrogen bonds       : bond        0.03177 (   24)
  hydrogen bonds       : angle       6.82173 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.133 
Fit side-chains
REVERT: F   43 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8120 (mttm)
REVERT: J   43 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8042 (mttp)
  outliers start: 10
  outliers final: 5
  residues processed: 69
  average time/residue: 0.0684
  time to fit residues: 5.7239
Evaluate side-chains
  59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain I residue   81 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 47 optimal weight:    0.1980
   chunk 33 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 0 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0570
   chunk 45 optimal weight:    0.2980
   overall best weight:    1.4900

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
B  50 HIS
F  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.130402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.112795 restraints weight = 5014.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.36
r_work: 0.3473 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3830  Z= 0.105
  Angle     :  0.400   1.791   5190  Z= 0.247
  Chirality :  0.051   0.120    680
  Planarity :  0.002   0.008    650
  Dihedral  :  4.979  37.734    562
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 21.58 %
    Favored  : 76.84 %
  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 aren not related in a simple way.
  whole: -0.99 (0.36), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.75 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR B  39 
 PHE   0.008   0.002   PHE F  94 
 HIS   0.004   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3830)
  covalent geometry    : angle       0.40036 ( 5190)
  hydrogen bonds       : bond        0.03079 (   24)
  hydrogen bonds       : angle       6.30902 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.113 
Fit side-chains
REVERT: C   54 THR cc_start: 0.8877 (m) cc_final: 0.8656 (p)
REVERT: C   80 LYS cc_start: 0.8954 (tttp) cc_final: 0.8712 (tttm)
REVERT: E   46 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: F   43 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8231 (mttm)
REVERT: F   80 LYS cc_start: 0.8960 (tttp) cc_final: 0.8728 (tttt)
  outliers start: 6
  outliers final: 2
  residues processed: 64
  average time/residue: 0.0743
  time to fit residues: 5.6564
Evaluate side-chains
  56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 42 optimal weight:    0.5980
   chunk 35 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    3.0586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.105515 restraints weight = 5117.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.44
r_work: 0.3361 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3830  Z= 0.184
  Angle     :  0.441   2.214   5190  Z= 0.272
  Chirality :  0.052   0.124    680
  Planarity :  0.002   0.009    650
  Dihedral  :  5.094  13.980    560
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 21.05 %
    Favored  : 77.89 %
  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 aren not related in a simple way.
  whole: -1.32 (0.35), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.99 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3830)
  covalent geometry    : angle       0.44138 ( 5190)
  hydrogen bonds       : bond        0.03717 (   24)
  hydrogen bonds       : angle       6.13725 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C   54 THR cc_start: 0.8914 (m) cc_final: 0.8693 (p)
REVERT: F   43 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8247 (mttm)
REVERT: F   57 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8708 (mt-10)
REVERT: I   79 GLN cc_start: 0.9386 (tt0) cc_final: 0.9166 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.0664
  time to fit residues: 5.3472
Evaluate side-chains
  63 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.121968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.103199 restraints weight = 5127.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.37
r_work: 0.3322 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3830  Z= 0.272
  Angle     :  0.490   2.501   5190  Z= 0.301
  Chirality :  0.053   0.122    680
  Planarity :  0.002   0.009    650
  Dihedral  :  5.486  16.582    560
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.95 %
    Favored  : 78.42 %
  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 aren not related in a simple way.
  whole: -1.57 (0.34), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR F  39 
 PHE   0.008   0.002   PHE B  94 
 HIS   0.008   0.004   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 ( 3830)
  covalent geometry    : angle       0.49035 ( 5190)
  hydrogen bonds       : bond        0.04259 (   24)
  hydrogen bonds       : angle       6.10900 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.139 
Fit side-chains
REVERT: C   54 THR cc_start: 0.8974 (m) cc_final: 0.8697 (p)
REVERT: F   57 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8742 (mt-10)
REVERT: I   79 GLN cc_start: 0.9442 (tt0) cc_final: 0.9225 (tt0)
  outliers start: 10
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0616
  time to fit residues: 5.3116
Evaluate side-chains
  68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.128589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.111698 restraints weight = 4961.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.23
r_work: 0.3497 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   3830  Z= 0.084
  Angle     :  0.376   2.132   5190  Z= 0.230
  Chirality :  0.050   0.120    680
  Planarity :  0.001   0.006    650
  Dihedral  :  4.388  12.300    560
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.21 %
    Favored  : 78.95 %
  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 aren not related in a simple way.
  whole: -1.40 (0.36), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.06 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR G  39 
 PHE   0.005   0.001   PHE I  94 
 HIS   0.004   0.002   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 ( 3830)
  covalent geometry    : angle       0.37648 ( 5190)
  hydrogen bonds       : bond        0.02854 (   24)
  hydrogen bonds       : angle       5.66946 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   94 PHE cc_start: 0.7188 (m-10) cc_final: 0.6982 (t80)
REVERT: F   43 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8346 (mttm)
REVERT: F   57 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8743 (mt-10)
REVERT: I   79 GLN cc_start: 0.9386 (tt0) cc_final: 0.9183 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0788
  time to fit residues: 5.6022
Evaluate side-chains
  56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain I residue   81 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0570
   chunk 2 optimal weight:    2.9990
   overall best weight:    3.6106

-------------------------------------------------------------------------------
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 = 0.3716 r_free = 0.3716 target = 0.122789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.105060 restraints weight = 5013.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.25
r_work: 0.3397 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   3830  Z= 0.216
  Angle     :  0.440   2.369   5190  Z= 0.271
  Chirality :  0.052   0.123    680
  Planarity :  0.002   0.008    650
  Dihedral  :  4.972  14.240    560
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.68 %
    Favored  : 78.42 %
  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 aren not related in a simple way.
  whole: -1.54 (0.35), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.16 (0.26), residues: 540

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 3830)
  covalent geometry    : angle       0.44043 ( 5190)
  hydrogen bonds       : bond        0.03889 (   24)
  hydrogen bonds       : angle       5.90671 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B   94 PHE cc_start: 0.7296 (m-10) cc_final: 0.7001 (t80)
REVERT: F   43 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8259 (mttm)
REVERT: F   57 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8827 (mt-10)
REVERT: I   79 GLN cc_start: 0.9454 (tt0) cc_final: 0.9252 (tt0)
  outliers start: 11
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0690
  time to fit residues: 5.6114
Evaluate side-chains
  67 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.7188

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.122327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.104830 restraints weight = 4967.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.23
r_work: 0.3387 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3830  Z= 0.222
  Angle     :  0.448   2.356   5190  Z= 0.275
  Chirality :  0.052   0.123    680
  Planarity :  0.002   0.008    650
  Dihedral  :  5.091  14.387    560
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.16 %
    Favored  : 78.68 %
  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 aren not related in a simple way.
  whole: -1.58 (0.34), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  39 
 PHE   0.005   0.002   PHE B  94 
 HIS   0.007   0.004   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 3830)
  covalent geometry    : angle       0.44823 ( 5190)
  hydrogen bonds       : bond        0.03960 (   24)
  hydrogen bonds       : angle       5.94250 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.103 
Fit side-chains
REVERT: B   94 PHE cc_start: 0.7402 (m-10) cc_final: 0.7000 (t80)
  outliers start: 12
  outliers final: 12
  residues processed: 68
  average time/residue: 0.0647
  time to fit residues: 5.4615
Evaluate side-chains
  70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 34 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0270
   chunk 45 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.8844

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.123281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105830 restraints weight = 4937.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.24
r_work: 0.3406 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3830  Z= 0.176
  Angle     :  0.421   2.183   5190  Z= 0.259
  Chirality :  0.051   0.124    680
  Planarity :  0.002   0.008    650
  Dihedral  :  4.868  13.253    560
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.74 %
    Favored  : 77.37 %
  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 aren not related in a simple way.
  whole: -1.55 (0.34), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.17 (0.26), residues: 540

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3830)
  covalent geometry    : angle       0.42060 ( 5190)
  hydrogen bonds       : bond        0.03706 (   24)
  hydrogen bonds       : angle       5.84300 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B   94 PHE cc_start: 0.7402 (m-10) cc_final: 0.6938 (t80)
  outliers start: 11
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0721
  time to fit residues: 5.9491
Evaluate side-chains
  69 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.2980
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.125576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.108027 restraints weight = 4908.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.27
r_work: 0.3442 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   3830  Z= 0.123
  Angle     :  0.389   2.008   5190  Z= 0.239
  Chirality :  0.051   0.123    680
  Planarity :  0.001   0.006    650
  Dihedral  :  4.519  12.393    560
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.47 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.34), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.12 (0.26), residues: 540

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3830)
  covalent geometry    : angle       0.38912 ( 5190)
  hydrogen bonds       : bond        0.03297 (   24)
  hydrogen bonds       : angle       5.67998 (   72)

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B   94 PHE cc_start: 0.7375 (m-10) cc_final: 0.6881 (t80)
  outliers start: 11
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0748
  time to fit residues: 5.5804
Evaluate side-chains
  63 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.122956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.105677 restraints weight = 4879.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.19
r_work: 0.3401 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   3830  Z= 0.201
  Angle     :  0.431   2.282   5190  Z= 0.265
  Chirality :  0.052   0.120    680
  Planarity :  0.002   0.008    650
  Dihedral  :  4.872  13.374    560
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.74 %
    Favored  : 77.37 %
  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 aren not related in a simple way.
  whole: -1.57 (0.34), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.18 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  39 
 PHE   0.005   0.002   PHE I  94 
 HIS   0.006   0.003   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 3830)
  covalent geometry    : angle       0.43095 ( 5190)
  hydrogen bonds       : bond        0.03816 (   24)
  hydrogen bonds       : angle       5.83092 (   72)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 942.00 seconds
wall clock time: 16 minutes 51.56 seconds (1011.56 seconds total)