Starting phenix.real_space_refine
on Fri Aug 22 15:22:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ol3_16944/08_2025/8ol3_16944.cif"
  }
  resolution = 3.5
  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=   0.280 sd=   1.397
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: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1610      2.51       5
     N     410      2.21       5
     O     440      1.98       5
     H    2500      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  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: 4970
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 497
          Classifications: {'peptide': 33}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 32}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.88, per 1000 atoms: 0.18
  Number of scatterers: 4970
  At special positions: 0
  Unit cell: (61.2, 90.576, 39.168, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     440      8.00
     N     410      7.00
     C    1610      6.00
     H    2500      1.00
    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: 0.56
  Conformation dependent library (CDL) restraints added in 129.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  560

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 60.6% 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 11 through 21
      removed outlier: 7.049A  pdb=" N   VAL C  12 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   HIS A  13 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   HIS C  14 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL E  12 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   HIS C  13 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   HIS E  14 " --> pdb=" O   HIS C  13 " (cutoff:3.500A)
      removed outlier: 9.161A  pdb=" N   GLU E  11 " --> pdb=" O   VAL G  12 " (cutoff:3.500A)
      removed outlier: 10.300A  pdb=" N   HIS G  14 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   HIS E  13 " --> pdb=" O   HIS G  14 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   LYS G  16 " --> pdb=" O   HIS E  13 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN E  15 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   VAL G  18 " --> pdb=" O   GLN E  15 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU E  17 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   PHE G  20 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   PHE E  19 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 9.121A  pdb=" N   GLU G  11 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 10.246A  pdb=" N   HIS I  14 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   HIS G  13 " --> pdb=" O   HIS I  14 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   LYS I  16 " --> pdb=" O   HIS G  13 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLN G  15 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL I  18 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU G  17 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   PHE I  20 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   PHE G  19 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27
      removed outlier: 8.596A  pdb=" N   VAL A  24 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ASN C  27 " --> pdb=" O   VAL A  24 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   SER A  26 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   SER C  26 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ASN E  27 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
      removed outlier: 8.645A  pdb=" N   VAL E  24 " --> pdb=" O   GLY G  25 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ASN G  27 " --> pdb=" O   VAL E  24 " (cutoff:3.500A)
      removed outlier: 8.808A  pdb=" N   SER E  26 " --> pdb=" O   ASN G  27 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   VAL G  24 " --> pdb=" O   GLY I  25 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASN I  27 " --> pdb=" O   VAL G  24 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   SER G  26 " --> pdb=" O   ASN I  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35
      removed outlier: 6.212A  pdb=" N   ILE A  31 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU C  34 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   GLY A  33 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU E  34 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   MET C  35 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE E  31 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   LEU G  34 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   GLY E  33 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE G  31 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU I  34 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   GLY G  33 " --> pdb=" O   LEU I  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41
      removed outlier: 6.447A  pdb=" N   VAL E  40 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 21
      removed outlier: 9.222A  pdb=" N   GLU B  11 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 10.342A  pdb=" N   HIS D  14 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   HIS B  13 " --> pdb=" O   HIS D  14 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   LYS D  16 " --> pdb=" O   HIS B  13 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   GLN B  15 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   VAL D  18 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU B  17 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   PHE D  20 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   PHE B  19 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   GLU D  11 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 10.314A  pdb=" N   HIS F  14 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   HIS D  13 " --> pdb=" O   HIS F  14 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   LYS F  16 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   GLN D  15 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   VAL F  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU D  17 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   PHE F  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   PHE D  19 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   GLU F  11 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 10.278A  pdb=" N   HIS H  14 " --> pdb=" O   GLU F  11 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   HIS F  13 " --> pdb=" O   HIS H  14 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   LYS H  16 " --> pdb=" O   HIS F  13 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   GLN F  15 " --> pdb=" O   LYS H  16 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   VAL H  18 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU F  17 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   PHE H  20 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   PHE F  19 " --> pdb=" O   PHE H  20 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   GLU H  11 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 9.780A  pdb=" N   HIS J  14 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   HIS H  13 " --> pdb=" O   HIS J  14 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   LYS J  16 " --> pdb=" O   HIS H  13 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   GLN H  15 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL J  18 " --> pdb=" O   GLN H  15 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   LEU H  17 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   PHE J  20 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   PHE H  19 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 27
      removed outlier: 8.627A  pdb=" N   VAL B  24 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ASN D  27 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 8.786A  pdb=" N   SER B  26 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   VAL D  24 " --> pdb=" O   GLY F  25 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ASN F  27 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   SER D  26 " --> pdb=" O   ASN F  27 " (cutoff:3.500A)
      removed outlier: 8.695A  pdb=" N   VAL F  24 " --> pdb=" O   GLY H  25 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   ASN H  27 " --> pdb=" O   VAL F  24 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   SER F  26 " --> pdb=" O   ASN H  27 " (cutoff:3.500A)
      removed outlier: 8.861A  pdb=" N   VAL H  24 " --> pdb=" O   GLY J  25 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ASN J  27 " --> pdb=" O   VAL H  24 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   SER H  26 " --> pdb=" O   ASN J  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35
      removed outlier: 6.242A  pdb=" N   ILE B  31 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU D  34 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   GLY B  33 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ILE D  31 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   LEU F  34 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   GLY D  33 " --> pdb=" O   LEU F  34 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ILE F  31 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   LEU H  34 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLY F  33 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ILE H  31 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU J  34 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   GLY H  33 " --> pdb=" O   LEU J  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41

    32 hydrogen bonds defined for protein.
    96 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: 1.25

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        0.84 -     1.17: 2470
        1.17 -     1.50: 1420
        1.50 -     1.83: 1100
        1.83 -     2.16: 10
        2.16 -     2.49: 10
  Bond restraints: 5010
  Sorted by residual:
  bond pdb=" CE1 HIS H  13 "
       pdb=" HE1 HIS H  13 "
    ideal  model  delta    sigma   weight residual
    0.930  2.489 -1.559 2.00e-02 2.50e+03 6.08e+03
  bond pdb=" CE1 HIS G  13 "
       pdb=" HD2 HIS G  13 "
    ideal  model  delta    sigma   weight residual
    0.930  2.489 -1.559 2.00e-02 2.50e+03 6.08e+03
  bond pdb=" CE1 HIS F  13 "
       pdb=" HD2 HIS F  13 "
    ideal  model  delta    sigma   weight residual
    0.930  2.489 -1.559 2.00e-02 2.50e+03 6.08e+03
  bond pdb=" CE1 HIS A  13 "
       pdb=" HE1 HIS A  13 "
    ideal  model  delta    sigma   weight residual
    0.930  2.489 -1.559 2.00e-02 2.50e+03 6.08e+03
  bond pdb=" CE1 HIS E  13 "
       pdb=" HD2 HIS E  13 "
    ideal  model  delta    sigma   weight residual
    0.930  2.489 -1.559 2.00e-02 2.50e+03 6.08e+03
  ... (remaining 5005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    22.09: 9010
       22.09 -    44.17: 20
       44.17 -    66.26: 0
       66.26 -    88.35: 0
       88.35 -   110.44: 30
  Bond angle restraints: 9060
  Sorted by residual:
  angle pdb=" CG  HIS J  13 "
        pdb=" CD2 HIS J  13 "
        pdb=" HD1 HIS J  13 "
      ideal   model   delta    sigma   weight residual
     126.40   15.96  110.44 3.00e+00 1.11e-01 1.36e+03
  angle pdb=" CG  HIS C  13 "
        pdb=" CD2 HIS C  13 "
        pdb=" HD1 HIS C  13 "
      ideal   model   delta    sigma   weight residual
     126.40   15.97  110.43 3.00e+00 1.11e-01 1.35e+03
  angle pdb=" CG  HIS D  13 "
        pdb=" CD2 HIS D  13 "
        pdb=" HD1 HIS D  13 "
      ideal   model   delta    sigma   weight residual
     126.40   15.98  110.42 3.00e+00 1.11e-01 1.35e+03
  angle pdb=" CG  HIS H  13 "
        pdb=" CD2 HIS H  13 "
        pdb=" HD2 HIS H  13 "
      ideal   model   delta    sigma   weight residual
     126.40   15.98  110.42 3.00e+00 1.11e-01 1.35e+03
  angle pdb=" CG  HIS F  13 "
        pdb=" CD2 HIS F  13 "
        pdb=" HD1 HIS F  13 "
      ideal   model   delta    sigma   weight residual
     126.40   15.98  110.42 3.00e+00 1.11e-01 1.35e+03
  ... (remaining 9055 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.66: 2180
       34.66 -    69.33: 90
       69.33 -   103.99: 10
      103.99 -   138.66: 0
      138.66 -   173.32: 30
  Dihedral angle restraints: 2310
    sinusoidal: 1220
      harmonic: 1090
  Sorted by residual:
  dihedral pdb=" CG  HIS C  13 "
           pdb=" ND1 HIS C  13 "
           pdb=" CE1 HIS C  13 "
           pdb=" HD2 HIS C  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00   -6.68 -173.32     0      5.00e+00 4.00e-02 1.20e+03
  dihedral pdb=" CG  HIS I  13 "
           pdb=" ND1 HIS I  13 "
           pdb=" CE1 HIS I  13 "
           pdb=" HD2 HIS I  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00   -6.68 -173.32     0      5.00e+00 4.00e-02 1.20e+03
  dihedral pdb=" CG  HIS A  13 "
           pdb=" ND1 HIS A  13 "
           pdb=" CE1 HIS A  13 "
           pdb=" HE1 HIS A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00   -6.70 -173.30     0      5.00e+00 4.00e-02 1.20e+03
  ... (remaining 2307 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 221
       0.027 -    0.054: 66
       0.054 -    0.081: 20
       0.081 -    0.108: 33
       0.108 -    0.135: 50
  Chirality restraints: 390
  Sorted by residual:
  chirality pdb=" CA  ILE H  31 "
            pdb=" N   ILE H  31 "
            pdb=" C   ILE H  31 "
            pdb=" CB  ILE H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  ILE A  31 "
            pdb=" N   ILE A  31 "
            pdb=" C   ILE A  31 "
            pdb=" CB  ILE A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE F  31 "
            pdb=" N   ILE F  31 "
            pdb=" C   ILE F  31 "
            pdb=" CB  ILE F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 387 not shown)

  Planarity restraints: 750
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS I  13 "   -0.004 2.00e-02 2.50e+03   5.59e-02 7.03e+01
        pdb=" CG  HIS I  13 "    0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS I  13 "   -0.095 2.00e-02 2.50e+03
        pdb=" CD2 HIS I  13 "   -0.070 2.00e-02 2.50e+03
        pdb=" CE1 HIS I  13 "    0.032 2.00e-02 2.50e+03
        pdb=" NE2 HIS I  13 "    0.065 2.00e-02 2.50e+03
        pdb=" HD1 HIS I  13 "    0.090 2.00e-02 2.50e+03
        pdb=" HD2 HIS I  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 HIS I  13 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  13 "    0.004 2.00e-02 2.50e+03   5.58e-02 7.01e+01
        pdb=" CG  HIS H  13 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  13 "    0.095 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  13 "    0.070 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  13 "   -0.032 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" HD2 HIS H  13 "   -0.089 2.00e-02 2.50e+03
        pdb=" HE1 HIS H  13 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 HIS H  13 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS J  13 "    0.004 2.00e-02 2.50e+03   5.58e-02 6.99e+01
        pdb=" CG  HIS J  13 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND1 HIS J  13 "    0.095 2.00e-02 2.50e+03
        pdb=" CD2 HIS J  13 "    0.069 2.00e-02 2.50e+03
        pdb=" CE1 HIS J  13 "   -0.032 2.00e-02 2.50e+03
        pdb=" NE2 HIS J  13 "   -0.066 2.00e-02 2.50e+03
        pdb=" HD1 HIS J  13 "   -0.089 2.00e-02 2.50e+03
        pdb=" HD2 HIS J  13 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 HIS J  13 "    0.026 2.00e-02 2.50e+03
  ... (remaining 747 not shown)

  Histogram of nonbonded interaction distances:
        0.69 -     1.48: 20
        1.48 -     2.26: 803
        2.26 -     3.04: 14642
        3.04 -     3.82: 20572
        3.82 -     4.60: 33806
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 69843
  Sorted by model distance:
  nonbonded pdb=" CD2 HIS D  13 "
            pdb=" HD2 HIS D  13 "
     model   vdw
     0.694 2.240
  nonbonded pdb=" CD2 HIS J  13 "
            pdb=" HD2 HIS J  13 "
     model   vdw
     0.695 2.240
  nonbonded pdb=" CD2 HIS E  13 "
            pdb=" HD2 HIS E  13 "
     model   vdw
     0.695 2.240
  nonbonded pdb=" CD2 HIS C  13 "
            pdb=" HD2 HIS C  13 "
     model   vdw
     0.695 2.240
  nonbonded pdb=" CD2 HIS B  13 "
            pdb=" HD2 HIS B  13 "
     model   vdw
     0.696 2.240
  ... (remaining 69838 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  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:             0.030
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.630
  Find NCS groups from input model:        0.060
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.098   2510  Z= 0.808
  Angle     :  0.671   5.540   3380  Z= 0.579
  Chirality :  0.057   0.135    390
  Planarity :  0.008   0.052    430
  Dihedral  :  9.518  37.061    850
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.18 (0.48), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.13 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR I  10 
 PHE   0.003   0.001   PHE J  19 
 HIS   0.069   0.023   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00868 ( 2510)
  covalent geometry    : angle       0.67140 ( 3380)
  hydrogen bonds       : bond        0.13654 (   32)
  hydrogen bonds       : angle       8.57717 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0615
  time to fit residues: 6.5890
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   overall best weight:    2.9384

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

Flipped N/Q/H residues before XYZ refinement:
E  14 HIS
B  14 HIS
C  14 HIS
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  14 HIS
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  14 HIS
J  14 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5272 r_free = 0.5272 target = 0.283341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5718 r_free = 0.5718 target = 0.244361 restraints weight = 13515.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.5762 r_free = 0.5762 target = 0.248429 restraints weight = 5900.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5783 r_free = 0.5783 target = 0.250758 restraints weight = 3165.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.5795 r_free = 0.5795 target = 0.252027 restraints weight = 1892.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5808 r_free = 0.5808 target = 0.252937 restraints weight = 1257.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.5263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4949 r_free = 0.4949    target_work(ls_wunit_k1) = 0.256         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4949 r_free = 0.4949    target_work(ls_wunit_k1) = 0.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2510  Z= 0.176
  Angle     :  0.472   2.974   3380  Z= 0.283
  Chirality :  0.059   0.153    390
  Planarity :  0.002   0.007    430
  Dihedral  :  5.874  19.107    340
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 11.20 %
    Favored  : 83.60 %
  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: -0.10 (0.50), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.07 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  10 
 PHE   0.015   0.003   PHE C  19 
 HIS   0.004   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 2510)
  covalent geometry    : angle       0.47188 ( 3380)
  hydrogen bonds       : bond        0.03494 (   32)
  hydrogen bonds       : angle       6.58688 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 13
  outliers final: 10
  residues processed: 51
  average time/residue: 0.0603
  time to fit residues: 4.3787
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain G residue   11 GLU
Chi-restraints excluded: chain G residue   27 ASN
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  14 HIS
F  14 HIS
H  14 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.252127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.183628 restraints weight = 12394.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5049 r_free = 0.5049 target = 0.191724 restraints weight = 4944.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5091 r_free = 0.5091 target = 0.196744 restraints weight = 2781.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5132 r_free = 0.5132 target = 0.200293 restraints weight = 1804.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5155 r_free = 0.5155 target = 0.202669 restraints weight = 1249.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.5082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2510  Z= 0.133
  Angle     :  0.423   2.450   3380  Z= 0.251
  Chirality :  0.059   0.147    390
  Planarity :  0.002   0.006    430
  Dihedral  :  6.094  21.256    340
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 12.80 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.15 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.10 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  10 
 PHE   0.010   0.002   PHE A  19 
 HIS   0.001   0.000   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2510)
  covalent geometry    : angle       0.42344 ( 3380)
  hydrogen bonds       : bond        0.02923 (   32)
  hydrogen bonds       : angle       6.38492 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 34
  time to evaluate  : 0.146 
Fit side-chains
  outliers start: 13
  outliers final: 8
  residues processed: 45
  average time/residue: 0.0608
  time to fit residues: 3.9938
Evaluate side-chains
  35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain G residue   11 GLU
Chi-restraints excluded: chain H residue   11 GLU
Chi-restraints excluded: chain H residue   27 ASN
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5034 r_free = 0.5034 target = 0.174339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.149545 restraints weight = 12274.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.155119 restraints weight = 4898.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.159322 restraints weight = 2776.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4929 r_free = 0.4929 target = 0.162006 restraints weight = 1834.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.164455 restraints weight = 1362.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2510  Z= 0.129
  Angle     :  0.422   2.528   3380  Z= 0.251
  Chirality :  0.059   0.153    390
  Planarity :  0.001   0.005    430
  Dihedral  :  6.122  21.691    340
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 14.40 %
    Favored  : 80.40 %
  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: -0.24 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.18 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR J  10 
 PHE   0.008   0.002   PHE A  19 
 HIS   0.002   0.000   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2510)
  covalent geometry    : angle       0.42222 ( 3380)
  hydrogen bonds       : bond        0.02559 (   32)
  hydrogen bonds       : angle       6.22772 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 28
  time to evaluate  : 0.147 
Fit side-chains
  outliers start: 13
  outliers final: 8
  residues processed: 41
  average time/residue: 0.0597
  time to fit residues: 3.6064
Evaluate side-chains
  35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain G residue   11 GLU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.171459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.146230 restraints weight = 13175.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.152042 restraints weight = 5263.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.155787 restraints weight = 3011.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.159149 restraints weight = 2058.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.161404 restraints weight = 1487.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.4963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2510  Z= 0.113
  Angle     :  0.402   2.242   3380  Z= 0.236
  Chirality :  0.059   0.143    390
  Planarity :  0.001   0.005    430
  Dihedral  :  5.905  20.668    340
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.80 %
    Favored  : 79.60 %
  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: -0.29 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.21 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  10 
 PHE   0.008   0.001   PHE C  19 
 HIS   0.001   0.000   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 2510)
  covalent geometry    : angle       0.40190 ( 3380)
  hydrogen bonds       : bond        0.02264 (   32)
  hydrogen bonds       : angle       5.96773 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.133 
Fit side-chains
REVERT: J   11 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7510 (pt0)
  outliers start: 9
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0571
  time to fit residues: 3.4122
Evaluate side-chains
  33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.171972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.146673 restraints weight = 13354.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.152403 restraints weight = 5431.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.156686 restraints weight = 3128.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.159861 restraints weight = 2073.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.161801 restraints weight = 1498.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2510  Z= 0.114
  Angle     :  0.394   2.265   3380  Z= 0.231
  Chirality :  0.058   0.153    390
  Planarity :  0.001   0.009    430
  Dihedral  :  5.818  20.511    340
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.20 %
    Favored  : 80.80 %
  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: -0.33 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.24 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  10 
 PHE   0.008   0.001   PHE C  19 
 HIS   0.001   0.000   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 2510)
  covalent geometry    : angle       0.39351 ( 3380)
  hydrogen bonds       : bond        0.02160 (   32)
  hydrogen bonds       : angle       5.80841 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.145 
Fit side-chains
REVERT: J   11 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7363 (pt0)
  outliers start: 10
  outliers final: 8
  residues processed: 42
  average time/residue: 0.0553
  time to fit residues: 3.4203
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4971 r_free = 0.4971 target = 0.171726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.146278 restraints weight = 13182.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.152085 restraints weight = 5402.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.156179 restraints weight = 3076.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.159268 restraints weight = 2059.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.161500 restraints weight = 1490.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.4955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2510  Z= 0.118
  Angle     :  0.390   2.241   3380  Z= 0.229
  Chirality :  0.058   0.152    390
  Planarity :  0.001   0.006    430
  Dihedral  :  5.835  21.148    340
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.60 %
    Favored  : 80.80 %
  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: -0.37 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.27 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  10 
 PHE   0.008   0.001   PHE C  19 
 HIS   0.003   0.000   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 2510)
  covalent geometry    : angle       0.39006 ( 3380)
  hydrogen bonds       : bond        0.02121 (   32)
  hydrogen bonds       : angle       5.68541 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.164 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 38
  average time/residue: 0.0760
  time to fit residues: 4.1418
Evaluate side-chains
  36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.165552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.140303 restraints weight = 13555.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.145617 restraints weight = 5604.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.149700 restraints weight = 3280.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.153072 restraints weight = 2199.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.155356 restraints weight = 1599.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.019   2510  Z= 0.237
  Angle     :  0.470   3.190   3380  Z= 0.280
  Chirality :  0.058   0.155    390
  Planarity :  0.002   0.007    430
  Dihedral  :  7.618  34.666    340
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.40 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.57 (0.49), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.42 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR J  10 
 PHE   0.014   0.003   PHE C  19 
 HIS   0.003   0.001   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 2510)
  covalent geometry    : angle       0.46984 ( 3380)
  hydrogen bonds       : bond        0.02664 (   32)
  hydrogen bonds       : angle       6.18567 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.150 
Fit side-chains
  outliers start: 9
  outliers final: 9
  residues processed: 37
  average time/residue: 0.0584
  time to fit residues: 3.2327
Evaluate side-chains
  36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.169679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.144276 restraints weight = 13443.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.150102 restraints weight = 5420.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.154261 restraints weight = 3108.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.157335 restraints weight = 2091.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.159831 restraints weight = 1548.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2510  Z= 0.101
  Angle     :  0.393   2.163   3380  Z= 0.228
  Chirality :  0.058   0.142    390
  Planarity :  0.001   0.006    430
  Dihedral  :  6.326  25.269    340
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.20 %
    Favored  : 79.20 %
  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: -0.64 (0.48), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.48 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  10 
 PHE   0.007   0.001   PHE C  19 
 HIS   0.001   0.000   HIS J  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 2510)
  covalent geometry    : angle       0.39268 ( 3380)
  hydrogen bonds       : bond        0.02054 (   32)
  hydrogen bonds       : angle       5.58718 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.148 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0592
  time to fit residues: 3.1811
Evaluate side-chains
  33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0050
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0470
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.5033 r_free = 0.5033 target = 0.178264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.153071 restraints weight = 13146.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.159141 restraints weight = 5168.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.163641 restraints weight = 2940.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.166998 restraints weight = 1937.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.169454 restraints weight = 1385.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   2510  Z= 0.070
  Angle     :  0.380   1.938   3380  Z= 0.218
  Chirality :  0.059   0.149    390
  Planarity :  0.001   0.005    430
  Dihedral  :  4.963  12.799    340
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 20.00 %
    Favored  : 78.80 %
  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: -0.71 (0.48), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.53 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR I  10 
 PHE   0.005   0.001   PHE C  19 
 HIS   0.001   0.000   HIS I  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00150 ( 2510)
  covalent geometry    : angle       0.37960 ( 3380)
  hydrogen bonds       : bond        0.01703 (   32)
  hydrogen bonds       : angle       5.08486 (   96)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: J   11 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7631 (pt0)
  outliers start: 3
  outliers final: 2
  residues processed: 37
  average time/residue: 0.0589
  time to fit residues: 3.2967
Evaluate side-chains
  32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain J residue   11 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.5029 r_free = 0.5029 target = 0.177438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.152321 restraints weight = 13295.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.158358 restraints weight = 5215.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.162760 restraints weight = 2930.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.166105 restraints weight = 1937.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.168347 restraints weight = 1380.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.5004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   2510  Z= 0.082
  Angle     :  0.374   2.405   3380  Z= 0.216
  Chirality :  0.058   0.137    390
  Planarity :  0.001   0.004    430
  Dihedral  :  5.090  15.339    340
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 20.40 %
    Favored  : 78.40 %
  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: -0.70 (0.47), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.52 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR J  10 
 PHE   0.006   0.001   PHE A  20 
 HIS   0.001   0.000   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 2510)
  covalent geometry    : angle       0.37358 ( 3380)
  hydrogen bonds       : bond        0.01702 (   32)
  hydrogen bonds       : angle       5.04118 (   96)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1492.66 seconds
wall clock time: 26 minutes 5.57 seconds (1565.57 seconds total)