Starting phenix.real_space_refine
on Wed Sep 17 03:00:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzw_51735/09_2025/9gzw_51735.map"
  }
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1332      2.51       5
     N     384      2.21       5
     O     444      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2160
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 179
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 0.51, per 1000 atoms: 0.24
  Number of scatterers: 2160
  At special positions: 0
  Unit cell: (72.265, 70.03, 43.955, 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     444      8.00
     N     384      7.00
     C    1332      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=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 84.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  528

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 58.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 22
      removed outlier: 6.306A  pdb=" N   PHE A  15 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   HIS C  18 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL A  17 " --> pdb=" O   HIS C  18 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   SER C  20 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   SER A  19 " --> pdb=" O   SER C  20 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ASN C  22 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ASN A  21 " --> pdb=" O   ASN C  22 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   PHE C  15 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   HIS E  18 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL C  17 " --> pdb=" O   HIS E  18 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   SER E  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   SER C  19 " --> pdb=" O   SER E  20 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ASN E  22 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASN C  21 " --> pdb=" O   ASN E  22 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   PHE E  15 " --> pdb=" O   LEU G  16 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   HIS G  18 " --> pdb=" O   PHE E  15 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL E  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   SER G  20 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   SER E  19 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   ASN G  22 " --> pdb=" O   SER E  19 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ASN E  21 " --> pdb=" O   ASN G  22 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   PHE G  15 " --> pdb=" O   LEU I  16 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   HIS I  18 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL G  17 " --> pdb=" O   HIS I  18 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   SER I  20 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   SER G  19 " --> pdb=" O   SER I  20 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   ASN I  22 " --> pdb=" O   SER G  19 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ASN G  21 " --> pdb=" O   ASN I  22 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   PHE I  15 " --> pdb=" O   LEU K  16 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   HIS K  18 " --> pdb=" O   PHE I  15 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL I  17 " --> pdb=" O   HIS K  18 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   SER K  20 " --> pdb=" O   VAL I  17 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   SER I  19 " --> pdb=" O   SER K  20 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ASN K  22 " --> pdb=" O   SER I  19 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASN I  21 " --> pdb=" O   ASN K  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33
      removed outlier: 6.493A  pdb=" N   LEU A  27 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR C  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   SER A  29 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL C  32 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ASN A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU C  27 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   THR E  30 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   SER C  29 " --> pdb=" O   THR E  30 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   VAL E  32 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ASN C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU E  27 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   THR G  30 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   SER E  29 " --> pdb=" O   THR G  30 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL G  32 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ASN E  31 " --> pdb=" O   VAL G  32 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU G  27 " --> pdb=" O   SER I  28 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   THR I  30 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   SER G  29 " --> pdb=" O   THR I  30 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   VAL I  32 " --> pdb=" O   SER G  29 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ASN G  31 " --> pdb=" O   VAL I  32 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU I  27 " --> pdb=" O   SER K  28 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   THR K  30 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   SER I  29 " --> pdb=" O   THR K  30 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   VAL K  32 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASN I  31 " --> pdb=" O   VAL K  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 22
      removed outlier: 6.263A  pdb=" N   PHE B  15 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   HIS D  18 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL B  17 " --> pdb=" O   HIS D  18 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   SER D  20 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   SER B  19 " --> pdb=" O   SER D  20 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   ASN D  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASN B  21 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   PHE D  15 " --> pdb=" O   LEU F  16 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   HIS F  18 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL D  17 " --> pdb=" O   HIS F  18 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   SER F  20 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   SER D  19 " --> pdb=" O   SER F  20 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   ASN F  22 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ASN D  21 " --> pdb=" O   ASN F  22 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   PHE F  15 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   HIS H  18 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL F  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   SER H  20 " --> pdb=" O   VAL F  17 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   SER F  19 " --> pdb=" O   SER H  20 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   ASN H  22 " --> pdb=" O   SER F  19 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ASN F  21 " --> pdb=" O   ASN H  22 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   PHE H  15 " --> pdb=" O   LEU J  16 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   HIS J  18 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL H  17 " --> pdb=" O   HIS J  18 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   SER J  20 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER H  19 " --> pdb=" O   SER J  20 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   ASN J  22 " --> pdb=" O   SER H  19 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ASN H  21 " --> pdb=" O   ASN J  22 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   PHE J  15 " --> pdb=" O   LEU L  16 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   HIS L  18 " --> pdb=" O   PHE J  15 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL J  17 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   SER L  20 " --> pdb=" O   VAL J  17 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   SER J  19 " --> pdb=" O   SER L  20 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   ASN L  22 " --> pdb=" O   SER J  19 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASN J  21 " --> pdb=" O   ASN L  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33
      removed outlier: 6.496A  pdb=" N   LEU B  27 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   THR D  30 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER B  29 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   VAL D  32 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LEU D  27 " --> pdb=" O   SER F  28 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   THR F  30 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   SER D  29 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   VAL F  32 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN D  31 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LEU F  27 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR H  30 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   SER F  29 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   VAL H  32 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN F  31 " --> pdb=" O   VAL H  32 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU H  27 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   THR J  30 " --> pdb=" O   LEU H  27 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   SER H  29 " --> pdb=" O   THR J  30 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   VAL J  32 " --> pdb=" O   SER H  29 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN H  31 " --> pdb=" O   VAL J  32 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU J  27 " --> pdb=" O   SER L  28 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   THR L  30 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   SER J  29 " --> pdb=" O   THR L  30 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   VAL L  32 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ASN J  31 " --> pdb=" O   VAL L  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    No hydrogen bonds 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: 0.03

  Time building geometry restraints manager: 0.27 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: 348
        1.29 -     1.35: 368
        1.35 -     1.42: 269
        1.42 -     1.48: 359
        1.48 -     1.54: 840
  Bond restraints: 2184
  Sorted by residual:
  bond pdb=" N   GLY E  24 "
       pdb=" CA  GLY E  24 "
    ideal  model  delta    sigma   weight residual
    1.456  1.450  0.006 1.16e-02 7.43e+03 2.29e-01
  bond pdb=" CE1 PHE F  15 "
       pdb=" CZ  PHE F  15 "
    ideal  model  delta    sigma   weight residual
    1.382  1.368  0.014 3.00e-02 1.11e+03 2.06e-01
  bond pdb=" CE1 PHE E  15 "
       pdb=" CZ  PHE E  15 "
    ideal  model  delta    sigma   weight residual
    1.382  1.369  0.013 3.00e-02 1.11e+03 1.98e-01
  bond pdb=" CE1 PHE D  15 "
       pdb=" CZ  PHE D  15 "
    ideal  model  delta    sigma   weight residual
    1.382  1.369  0.013 3.00e-02 1.11e+03 1.95e-01
  bond pdb=" CE1 PHE H  15 "
       pdb=" CZ  PHE H  15 "
    ideal  model  delta    sigma   weight residual
    1.382  1.369  0.013 3.00e-02 1.11e+03 1.95e-01
  ... (remaining 2179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 2801
        1.62 -     3.24: 139
        3.24 -     4.86: 12
        4.86 -     6.48: 0
        6.48 -     8.10: 12
  Bond angle restraints: 2964
  Sorted by residual:
  angle pdb=" CA  LEU L  16 "
        pdb=" CB  LEU L  16 "
        pdb=" CG  LEU L  16 "
      ideal   model   delta    sigma   weight residual
     116.30  124.40   -8.10 3.50e+00 8.16e-02 5.36e+00
  angle pdb=" CA  LEU J  16 "
        pdb=" CB  LEU J  16 "
        pdb=" CG  LEU J  16 "
      ideal   model   delta    sigma   weight residual
     116.30  124.39   -8.09 3.50e+00 8.16e-02 5.35e+00
  angle pdb=" CA  LEU I  16 "
        pdb=" CB  LEU I  16 "
        pdb=" CG  LEU I  16 "
      ideal   model   delta    sigma   weight residual
     116.30  124.39   -8.09 3.50e+00 8.16e-02 5.34e+00
  angle pdb=" CA  LEU D  16 "
        pdb=" CB  LEU D  16 "
        pdb=" CG  LEU D  16 "
      ideal   model   delta    sigma   weight residual
     116.30  124.39   -8.09 3.50e+00 8.16e-02 5.34e+00
  angle pdb=" CA  LEU E  16 "
        pdb=" CB  LEU E  16 "
        pdb=" CG  LEU E  16 "
      ideal   model   delta    sigma   weight residual
     116.30  124.39   -8.09 3.50e+00 8.16e-02 5.34e+00
  ... (remaining 2959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.78: 1008
        6.78 -    13.56: 96
       13.56 -    20.34: 24
       20.34 -    27.12: 48
       27.12 -    33.90: 36
  Dihedral angle restraints: 1212
    sinusoidal: 396
      harmonic: 816
  Sorted by residual:
  dihedral pdb=" CA  LEU L  27 "
           pdb=" CB  LEU L  27 "
           pdb=" CG  LEU L  27 "
           pdb=" CD1 LEU L  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.02   32.98     3      1.50e+01 4.44e-03 5.48e+00
  dihedral pdb=" CA  LEU G  27 "
           pdb=" CB  LEU G  27 "
           pdb=" CG  LEU G  27 "
           pdb=" CD1 LEU G  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.03   32.97     3      1.50e+01 4.44e-03 5.48e+00
  dihedral pdb=" CA  LEU K  27 "
           pdb=" CB  LEU K  27 "
           pdb=" CG  LEU K  27 "
           pdb=" CD1 LEU K  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  147.04   32.96     3      1.50e+01 4.44e-03 5.47e+00
  ... (remaining 1209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 225
       0.040 -    0.079: 87
       0.079 -    0.119: 24
       0.119 -    0.158: 0
       0.158 -    0.198: 12
  Chirality restraints: 348
  Sorted by residual:
  chirality pdb=" CA  PHE J  15 "
            pdb=" N   PHE J  15 "
            pdb=" C   PHE J  15 "
            pdb=" CB  PHE J  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CA  PHE F  15 "
            pdb=" N   PHE F  15 "
            pdb=" C   PHE F  15 "
            pdb=" CB  PHE F  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.68e-01
  chirality pdb=" CA  PHE K  15 "
            pdb=" N   PHE K  15 "
            pdb=" C   PHE K  15 "
            pdb=" CB  PHE K  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.60e-01
  ... (remaining 345 not shown)

  Planarity restraints: 384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE J  15 "    0.002 2.00e-02 2.50e+03   1.84e-02 5.95e+00
        pdb=" CG  PHE J  15 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE J  15 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE J  15 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE J  15 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 PHE J  15 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE J  15 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I  15 "   -0.002 2.00e-02 2.50e+03   1.84e-02 5.91e+00
        pdb=" CG  PHE I  15 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE I  15 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE I  15 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE I  15 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 PHE I  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE I  15 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  15 "   -0.002 2.00e-02 2.50e+03   1.84e-02 5.90e+00
        pdb=" CG  PHE C  15 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  15 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  15 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  15 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  15 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  15 "    0.001 2.00e-02 2.50e+03
  ... (remaining 381 not shown)

  Histogram of nonbonded interaction distances:
        2.67 -     3.12: 1634
        3.12 -     3.56: 2123
        3.56 -     4.01: 3245
        4.01 -     4.45: 3789
        4.45 -     4.90: 7184
  Nonbonded interactions: 17975
  Sorted by model distance:
  nonbonded pdb=" N   NH2 H  38 "
            pdb=" O   TYR J  37 "
     model   vdw
     2.673 3.120
  nonbonded pdb=" N   SER B  34 "
            pdb=" OG  SER B  34 "
     model   vdw
     2.691 2.496
  nonbonded pdb=" N   SER E  34 "
            pdb=" OG  SER E  34 "
     model   vdw
     2.692 2.496
  nonbonded pdb=" N   SER I  34 "
            pdb=" OG  SER I  34 "
     model   vdw
     2.692 2.496
  nonbonded pdb=" N   SER K  34 "
            pdb=" OG  SER K  34 "
     model   vdw
     2.692 2.496
  ... (remaining 17970 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'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             3.520
  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:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.140
  Find NCS groups from input model:        0.020
  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:7.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
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      :  0.008   0.102   2196  Z= 0.758
  Angle     :  0.850   8.102   2964  Z= 0.419
  Chirality :  0.058   0.198    348
  Planarity :  0.004   0.018    384
  Dihedral  : 11.342  33.900    684
  Min Nonbonded Distance : 2.673

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  :  9.52 %
    Favored  : 85.71 %
  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: -2.72 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.28), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR D  37 
 PHE   0.033   0.008   PHE J  15 
 HIS   0.001   0.001   HIS G  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 2184)
  covalent geometry    : angle       0.84972 ( 2964)
  Misc. bond           : bond        0.10147 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 17
  time to evaluate  : 0.053 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 29
  average time/residue: 0.0699
  time to fit residues: 2.4086
Evaluate side-chains
  25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0670
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    4.2126

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
B  35 ASN
E  35 ASN
G  35 ASN
H  35 ASN
I  35 ASN
J  35 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.101846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.078581 restraints weight = 2705.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.94
r_work: 0.3267 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.026   2196  Z= 0.277
  Angle     :  0.648   5.744   2964  Z= 0.319
  Chirality :  0.053   0.119    348
  Planarity :  0.002   0.006    384
  Dihedral  :  4.851  17.392    296
  Min Nonbonded Distance : 2.681

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.59 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.28), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.22), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR J  37 
 PHE   0.009   0.003   PHE K  15 
 HIS   0.004   0.002   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 2184)
  covalent geometry    : angle       0.64828 ( 2964)
  Misc. bond           : bond        0.00195 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 2
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 3
  average time/residue: 0.0788
  time to fit residues: 0.3896
Evaluate side-chains
  3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 2
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
E  35 ASN
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.100993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.077445 restraints weight = 2777.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.99
r_work: 0.3285 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2196  Z= 0.244
  Angle     :  0.585   5.028   2964  Z= 0.291
  Chirality :  0.049   0.115    348
  Planarity :  0.002   0.005    384
  Dihedral  :  4.411   8.790    288
  Min Nonbonded Distance : 2.684

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  1.59 %
    Favored  : 97.62 %
  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: -3.83 (0.30), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.23), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  37 
 PHE   0.010   0.003   PHE L  15 
 HIS   0.003   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 2184)
  covalent geometry    : angle       0.58490 ( 2964)
  Misc. bond           : bond        0.00143 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 3
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 5
  average time/residue: 0.0725
  time to fit residues: 0.5337
Evaluate side-chains
  5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 3
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
F  35 ASN
G  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.101651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.078266 restraints weight = 2694.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.98
r_work: 0.3309 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   2196  Z= 0.125
  Angle     :  0.477   4.446   2964  Z= 0.232
  Chirality :  0.046   0.112    348
  Planarity :  0.001   0.004    384
  Dihedral  :  3.570   7.360    288
  Min Nonbonded Distance : 2.694

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  4.37 %
    Favored  : 95.24 %
  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: -3.91 (0.33), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.25), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR G  37 
 PHE   0.009   0.002   PHE F  15 
 HIS   0.002   0.001   HIS I  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2184)
  covalent geometry    : angle       0.47707 ( 2964)
  Misc. bond           : bond        0.00065 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  4 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 3
  time to evaluate  : 0.103 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 4
  average time/residue: 0.0870
  time to fit residues: 0.5396
Evaluate side-chains
  3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 2
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
I  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.099344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.076491 restraints weight = 2945.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.00
r_work: 0.3275 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2196  Z= 0.245
  Angle     :  0.535   4.282   2964  Z= 0.273
  Chirality :  0.048   0.114    348
  Planarity :  0.002   0.005    384
  Dihedral  :  4.278   8.379    288
  Min Nonbonded Distance : 2.686

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  5.95 %
    Favored  : 93.25 %
  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: -4.09 (0.34), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.26), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR E  37 
 PHE   0.010   0.003   PHE E  15 
 HIS   0.003   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 2184)
  covalent geometry    : angle       0.53490 ( 2964)
  Misc. bond           : bond        0.00134 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 3
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 5
  average time/residue: 0.0850
  time to fit residues: 0.6158
Evaluate side-chains
  5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 3
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.099434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.076572 restraints weight = 2965.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.96
r_work: 0.3276 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2196  Z= 0.201
  Angle     :  0.496   4.061   2964  Z= 0.255
  Chirality :  0.047   0.115    348
  Planarity :  0.002   0.004    384
  Dihedral  :  4.041   8.059    288
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.73 %
    Favored  : 90.48 %
  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: -4.02 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  37 
 PHE   0.010   0.002   PHE L  15 
 HIS   0.003   0.002   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 2184)
  covalent geometry    : angle       0.49634 ( 2964)
  Misc. bond           : bond        0.00114 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 1
  time to evaluate  : 0.085 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 3
  average time/residue: 0.0522
  time to fit residues: 0.3185
Evaluate side-chains
  3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 1
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.098475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.075029 restraints weight = 3161.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.99
r_work: 0.3233 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.029   2196  Z= 0.333
  Angle     :  0.576   3.978   2964  Z= 0.306
  Chirality :  0.049   0.115    348
  Planarity :  0.003   0.006    384
  Dihedral  :  4.748   9.422    288
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.11 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.28 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR I  37 
 PHE   0.012   0.003   PHE K  15 
 HIS   0.005   0.003   HIS B  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00666 ( 2184)
  covalent geometry    : angle       0.57622 ( 2964)
  Misc. bond           : bond        0.00182 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0939
  time to fit residues: 1.5627
Evaluate side-chains
  14 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0470
   chunk 14 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    3.6086

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.099002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075245 restraints weight = 3110.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.95
r_work: 0.3238 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2196  Z= 0.242
  Angle     :  0.522   3.827   2964  Z= 0.276
  Chirality :  0.046   0.116    348
  Planarity :  0.002   0.005    384
  Dihedral  :  4.240   8.892    288
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.90 %
    Favored  : 87.30 %
  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: -4.17 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.28), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  37 
 PHE   0.011   0.002   PHE K  15 
 HIS   0.003   0.002   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 2184)
  covalent geometry    : angle       0.52178 ( 2964)
  Misc. bond           : bond        0.00142 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 10
  average time/residue: 0.0985
  time to fit residues: 1.2083
Evaluate side-chains
  10 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 23 optimal weight:    0.0070
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    3.8006

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.099456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.074694 restraints weight = 4016.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.13
r_work: 0.3213 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   2196  Z= 0.254
  Angle     :  0.531   3.736   2964  Z= 0.282
  Chirality :  0.046   0.115    348
  Planarity :  0.002   0.005    384
  Dihedral  :  4.297   8.910    288
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.30 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.19 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.28), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  37 
 PHE   0.011   0.003   PHE K  15 
 HIS   0.004   0.002   HIS I  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 2184)
  covalent geometry    : angle       0.53113 ( 2964)
  Misc. bond           : bond        0.00147 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.085 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0983
  time to fit residues: 1.7372
Evaluate side-chains
  15 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0670
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.099245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.074864 restraints weight = 3051.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.96
r_work: 0.3230 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   2196  Z= 0.241
  Angle     :  0.522   3.676   2964  Z= 0.278
  Chirality :  0.046   0.115    348
  Planarity :  0.002   0.005    384
  Dihedral  :  4.222   9.052    288
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.30 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.22 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.28), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  37 
 PHE   0.012   0.003   PHE K  15 
 HIS   0.003   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 2184)
  covalent geometry    : angle       0.52226 ( 2964)
  Misc. bond           : bond        0.00143 (   12)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 13
  average time/residue: 0.0891
  time to fit residues: 1.3836
Evaluate side-chains
  13 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0570
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    5.2106

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.098863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.073725 restraints weight = 3462.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.07
r_work: 0.3202 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.031   2196  Z= 0.345
  Angle     :  0.582   3.901   2964  Z= 0.315
  Chirality :  0.048   0.116    348
  Planarity :  0.003   0.006    384
  Dihedral  :  4.574   9.803    288
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.30 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.26 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.28), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR B  37 
 PHE   0.013   0.003   PHE K  15 
 HIS   0.004   0.002   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 ( 2184)
  covalent geometry    : angle       0.58186 ( 2964)
  Misc. bond           : bond        0.00203 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 830.55 seconds
wall clock time: 14 minutes 56.39 seconds (896.39 seconds total)