Starting phenix.real_space_refine
on Fri Aug 22 12:56:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ynr_33969/08_2025/7ynr_33969_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    1590      2.51       5
     N     438      2.21       5
     O     498      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: 2526
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.52, per 1000 atoms: 0.21
  Number of scatterers: 2526
  At special positions: 0
  Unit cell: (101.352, 104.648, 31.312, 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     498      8.00
     N     438      7.00
     C    1590      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: 0.16
  Conformation dependent library (CDL) restraints added in 69.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 59.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39
      removed outlier: 6.851A  pdb=" N   LEU B  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 58
      removed outlier: 6.917A  pdb=" N   GLU C  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY A  47 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL C  52 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA A  53 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   THR C  54 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL A  55 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ALA C  56 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLU A  57 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   LYS C  58 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   GLU B  46 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   VAL C  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL B  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   GLY C  51 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 8.631A  pdb=" N   HIS B  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   ALA C  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   VAL B  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 10.441A  pdb=" N   VAL C  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 8.991A  pdb=" N   THR B  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 10.158A  pdb=" N   GLU C  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   ALA B  56 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66
      removed outlier: 6.567A  pdb=" N   GLN B  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   ASN C  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   THR B  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 82
      removed outlier: 6.325A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLY C  73 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   THR A  72 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   THR C  75 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   VAL A  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 9.284A  pdb=" N   VAL C  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ALA A  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   GLN C  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   THR C  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS A  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL C  74 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   THR B  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ALA C  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92
      removed outlier: 6.309A  pdb=" N   ALA A  90 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.176A  pdb=" N   VAL A  95 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 39
      removed outlier: 6.851A  pdb=" N   LEU E  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58
      removed outlier: 6.931A  pdb=" N   GLU F  46 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   GLY D  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL F  52 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ALA D  53 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   THR F  54 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL D  55 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA F  56 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   GLU D  57 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LYS F  58 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   GLU E  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.909A  pdb=" N   VAL F  49 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL E  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   GLY F  51 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 8.632A  pdb=" N   HIS E  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   ALA F  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 9.055A  pdb=" N   VAL E  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 10.439A  pdb=" N   VAL F  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 8.991A  pdb=" N   THR E  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 10.158A  pdb=" N   GLU F  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 9.050A  pdb=" N   ALA E  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66
      removed outlier: 6.566A  pdb=" N   GLN E  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   ASN F  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR E  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 82
      removed outlier: 6.337A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   GLY F  73 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 8.714A  pdb=" N   THR D  72 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   THR F  75 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 9.086A  pdb=" N   VAL D  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 9.292A  pdb=" N   VAL F  77 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA D  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   GLN F  79 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA D  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   THR F  81 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS D  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL F  74 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   THR E  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA F  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.305A  pdb=" N   ALA D  90 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96
      removed outlier: 6.175A  pdb=" N   VAL D  95 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)

    48 hydrogen bonds defined for protein.
    144 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: 0.40

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 432
        1.29 -     1.35: 396
        1.35 -     1.42: 102
        1.42 -     1.48: 414
        1.48 -     1.54: 1194
  Bond restraints: 2538
  Sorted by residual:
  bond pdb=" CG  LEU B  38 "
       pdb=" CD1 LEU B  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.11e-01
  bond pdb=" CG  LEU A  38 "
       pdb=" CD1 LEU A  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.00e-01
  bond pdb=" CG  LEU E  38 "
       pdb=" CD1 LEU E  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.501  0.020 3.30e-02 9.18e+02 3.79e-01
  bond pdb=" CG  LEU D  38 "
       pdb=" CD1 LEU D  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.501  0.020 3.30e-02 9.18e+02 3.76e-01
  bond pdb=" CG  LEU F  38 "
       pdb=" CD1 LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.501  0.020 3.30e-02 9.18e+02 3.72e-01
  ... (remaining 2533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.61: 2978
        0.61 -     1.22: 368
        1.22 -     1.84: 62
        1.84 -     2.45: 18
        2.45 -     3.06: 6
  Bond angle restraints: 3432
  Sorted by residual:
  angle pdb=" N   GLY B  73 "
        pdb=" CA  GLY B  73 "
        pdb=" C   GLY B  73 "
      ideal   model   delta    sigma   weight residual
     113.18  116.24   -3.06 2.37e+00 1.78e-01 1.67e+00
  angle pdb=" N   GLY C  73 "
        pdb=" CA  GLY C  73 "
        pdb=" C   GLY C  73 "
      ideal   model   delta    sigma   weight residual
     113.18  116.23   -3.05 2.37e+00 1.78e-01 1.66e+00
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     121.85  119.58    2.27 1.77e+00 3.19e-01 1.65e+00
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     121.85  119.58    2.27 1.77e+00 3.19e-01 1.64e+00
  angle pdb=" N   GLY E  73 "
        pdb=" CA  GLY E  73 "
        pdb=" C   GLY E  73 "
      ideal   model   delta    sigma   weight residual
     113.18  116.20   -3.02 2.37e+00 1.78e-01 1.62e+00
  ... (remaining 3427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.79: 1272
        8.79 -    17.59: 132
       17.59 -    26.38: 48
       26.38 -    35.18: 12
       35.18 -    43.97: 18
  Dihedral angle restraints: 1482
    sinusoidal: 492
      harmonic: 990
  Sorted by residual:
  dihedral pdb=" CA  THR D  72 "
           pdb=" C   THR D  72 "
           pdb=" N   GLY D  73 "
           pdb=" CA  GLY D  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.18   10.82     0      5.00e+00 4.00e-02 4.68e+00
  dihedral pdb=" CA  THR F  72 "
           pdb=" C   THR F  72 "
           pdb=" N   GLY F  73 "
           pdb=" CA  GLY F  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.19   10.81     0      5.00e+00 4.00e-02 4.67e+00
  dihedral pdb=" CA  THR A  72 "
           pdb=" C   THR A  72 "
           pdb=" N   GLY A  73 "
           pdb=" CA  GLY A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.20   10.80     0      5.00e+00 4.00e-02 4.67e+00
  ... (remaining 1479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 255
       0.025 -    0.050: 70
       0.050 -    0.075: 53
       0.075 -    0.100: 24
       0.100 -    0.125: 54
  Chirality restraints: 456
  Sorted by residual:
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  VAL F  49 "
            pdb=" N   VAL F  49 "
            pdb=" C   VAL F  49 "
            pdb=" CB  VAL F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 453 not shown)

  Planarity restraints: 420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  50 "   -0.007 2.00e-02 2.50e+03   5.91e-03 5.24e-01
        pdb=" CG  HIS A  50 "    0.012 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  50 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D  50 "    0.007 2.00e-02 2.50e+03   5.89e-03 5.20e-01
        pdb=" CG  HIS D  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" ND1 HIS D  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS D  50 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS D  50 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C  50 "   -0.007 2.00e-02 2.50e+03   5.87e-03 5.16e-01
        pdb=" CG  HIS C  50 "    0.012 2.00e-02 2.50e+03
        pdb=" ND1 HIS C  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS C  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS C  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS C  50 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 417 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 1003
        2.92 -     3.41: 2104
        3.41 -     3.91: 3991
        3.91 -     4.40: 4105
        4.40 -     4.90: 8617
  Nonbonded interactions: 19820
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS F  60 "
            pdb=" OE1 GLN F  62 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" NZ  LYS A  60 "
            pdb=" OE1 GLN A  62 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" NZ  LYS D  60 "
            pdb=" OE1 GLN D  62 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE1 GLN B  62 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" NZ  LYS C  60 "
            pdb=" OE1 GLN C  62 "
     model   vdw
     2.425 3.120
  ... (remaining 19815 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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:             3.500
  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:         0.020
  Set scattering table:                    0.000
  Process input model:                     3.420
  Find NCS groups from input model:        0.010
  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:5.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   12.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.003   0.021   2538  Z= 0.137
  Angle     :  0.459   3.058   3432  Z= 0.261
  Chirality :  0.052   0.125    456
  Planarity :  0.002   0.006    420
  Dihedral  : 10.047  43.973    858
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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: -3.30 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR E  39 
 PHE   0.009   0.002   PHE A  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2538)
  covalent geometry    : angle       0.45868 ( 3432)
  hydrogen bonds       : bond        0.19505 (   48)
  hydrogen bonds       : angle       9.22983 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.053 
Fit side-chains
REVERT: F   43 LYS cc_start: 0.8683 (mttt) cc_final: 0.8468 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.8377
  time to fit residues: 11.1083
Evaluate side-chains
  11 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.135692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.107758 restraints weight = 2760.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.07
r_work: 0.3658 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2538  Z= 0.108
  Angle     :  0.410   3.333   3432  Z= 0.238
  Chirality :  0.051   0.123    456
  Planarity :  0.001   0.007    420
  Dihedral  :  3.895  10.770    366
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  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: -2.70 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR F  39 
 PHE   0.009   0.002   PHE F  94 
 HIS   0.005   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2538)
  covalent geometry    : angle       0.40970 ( 3432)
  hydrogen bonds       : bond        0.02444 (   48)
  hydrogen bonds       : angle       7.03104 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.093 
Fit side-chains
REVERT: E   60 LYS cc_start: 0.8334 (tttp) cc_final: 0.8132 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.9667
  time to fit residues: 14.7563
Evaluate side-chains
  11 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.129699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.101557 restraints weight = 2888.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.10
r_work: 0.3527 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   2538  Z= 0.252
  Angle     :  0.505   4.547   3432  Z= 0.291
  Chirality :  0.052   0.122    456
  Planarity :  0.002   0.008    420
  Dihedral  :  4.474  13.141    366
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  8.14 %
    Favored  : 91.47 %
  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: -2.55 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR C  39 
 PHE   0.014   0.004   PHE F  94 
 HIS   0.007   0.004   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 2538)
  covalent geometry    : angle       0.50519 ( 3432)
  hydrogen bonds       : bond        0.03111 (   48)
  hydrogen bonds       : angle       7.01215 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.070 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 11
  average time/residue: 0.8392
  time to fit residues: 9.4258
Evaluate side-chains
  10 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.131243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.103166 restraints weight = 2854.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.11
r_work: 0.3577 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2538  Z= 0.164
  Angle     :  0.458   4.383   3432  Z= 0.264
  Chirality :  0.051   0.124    456
  Planarity :  0.002   0.008    420
  Dihedral  :  4.227  12.340    366
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  6.59 %
    Favored  : 91.09 %
  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: -2.27 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR F  39 
 PHE   0.011   0.003   PHE F  94 
 HIS   0.006   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2538)
  covalent geometry    : angle       0.45761 ( 3432)
  hydrogen bonds       : bond        0.02537 (   48)
  hydrogen bonds       : angle       6.73995 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.091 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 17
  average time/residue: 0.8187
  time to fit residues: 14.1788
Evaluate side-chains
  10 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 9
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.127423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.098685 restraints weight = 2892.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.15
r_work: 0.3468 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.045   2538  Z= 0.392
  Angle     :  0.647   5.395   3432  Z= 0.372
  Chirality :  0.057   0.128    456
  Planarity :  0.003   0.010    420
  Dihedral  :  4.977  13.856    366
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  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: -2.40 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR C  39 
 PHE   0.018   0.005   PHE F  94 
 HIS   0.009   0.005   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00931 ( 2538)
  covalent geometry    : angle       0.64739 ( 3432)
  hydrogen bonds       : bond        0.03398 (   48)
  hydrogen bonds       : angle       6.98123 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 1.0802
  time to fit residues: 9.9743
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.134040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.106736 restraints weight = 2827.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.07
r_work: 0.3594 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2538  Z= 0.101
  Angle     :  0.448   4.273   3432  Z= 0.258
  Chirality :  0.052   0.127    456
  Planarity :  0.001   0.007    420
  Dihedral  :  4.092  11.494    366
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.44), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.009   0.002   PHE F  94 
 HIS   0.005   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 2538)
  covalent geometry    : angle       0.44803 ( 3432)
  hydrogen bonds       : bond        0.02172 (   48)
  hydrogen bonds       : angle       6.48916 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.107 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 1.0256
  time to fit residues: 10.4737
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.129118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.101304 restraints weight = 2833.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.08
r_work: 0.3525 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   2538  Z= 0.283
  Angle     :  0.547   5.225   3432  Z= 0.313
  Chirality :  0.053   0.123    456
  Planarity :  0.002   0.009    420
  Dihedral  :  4.617  13.271    366
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -2.22 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR A  39 
 PHE   0.015   0.004   PHE C  94 
 HIS   0.008   0.004   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 ( 2538)
  covalent geometry    : angle       0.54666 ( 3432)
  hydrogen bonds       : bond        0.02961 (   48)
  hydrogen bonds       : angle       6.84945 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.096 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 1.2033
  time to fit residues: 11.0891
Evaluate side-chains
  9 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.132097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.104060 restraints weight = 2857.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.11
r_work: 0.3618 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2538  Z= 0.145
  Angle     :  0.456   4.603   3432  Z= 0.262
  Chirality :  0.052   0.125    456
  Planarity :  0.002   0.007    420
  Dihedral  :  4.211  12.079    366
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -2.06 (0.44), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  39 
 PHE   0.010   0.002   PHE F  94 
 HIS   0.006   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2538)
  covalent geometry    : angle       0.45592 ( 3432)
  hydrogen bonds       : bond        0.02393 (   48)
  hydrogen bonds       : angle       6.55991 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.099 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 8
  average time/residue: 1.0988
  time to fit residues: 8.9970
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.133797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.106263 restraints weight = 2896.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.11
r_work: 0.3593 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2538  Z= 0.107
  Angle     :  0.421   4.290   3432  Z= 0.243
  Chirality :  0.051   0.126    456
  Planarity :  0.001   0.007    420
  Dihedral  :  3.877  11.408    366
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.45), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.009   0.002   PHE F  94 
 HIS   0.005   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2538)
  covalent geometry    : angle       0.42066 ( 3432)
  hydrogen bonds       : bond        0.02183 (   48)
  hydrogen bonds       : angle       6.36977 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.091 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 1.0937
  time to fit residues: 10.0616
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.141716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.115014 restraints weight = 2781.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.06
r_work: 0.3708 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2538  Z= 0.098
  Angle     :  0.411   4.127   3432  Z= 0.238
  Chirality :  0.051   0.125    456
  Planarity :  0.001   0.006    420
  Dihedral  :  3.789  11.187    366
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.45), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.008   0.002   PHE F  94 
 HIS   0.005   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 2538)
  covalent geometry    : angle       0.41116 ( 3432)
  hydrogen bonds       : bond        0.02092 (   48)
  hydrogen bonds       : angle       6.20547 (  144)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.099 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 8
  average time/residue: 1.1534
  time to fit residues: 9.4752
Evaluate side-chains
  8 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    2.9986

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.130337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.102386 restraints weight = 2873.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.09
r_work: 0.3558 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   2538  Z= 0.238
  Angle     :  0.505   4.931   3432  Z= 0.290
  Chirality :  0.052   0.121    456
  Planarity :  0.002   0.009    420
  Dihedral  :  4.391  12.906    366
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  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: -2.10 (0.44), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR F  39 
 PHE   0.013   0.003   PHE C  94 
 HIS   0.008   0.004   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 2538)
  covalent geometry    : angle       0.50497 ( 3432)
  hydrogen bonds       : bond        0.02741 (   48)
  hydrogen bonds       : angle       6.67745 (  144)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 976.00 seconds
wall clock time: 17 minutes 31.12 seconds (1051.12 seconds total)