Starting phenix.real_space_refine
on Fri Aug 22 14:25:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zlp_60232/08_2025/8zlp_60232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zlp_60232/08_2025/8zlp_60232.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/8zlp_60232/08_2025/8zlp_60232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zlp_60232/08_2025/8zlp_60232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zlp_60232/08_2025/8zlp_60232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zlp_60232/08_2025/8zlp_60232.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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2574      2.51       5
     N     708      2.21       5
     O     822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 4116
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 686
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 98, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 97}
  Restraints were copied for chains:
    B, C, F, G, H
  Time building chain proxies: 0.83, per 1000 atoms: 0.20
  Number of scatterers: 4116
  At special positions: 0
  Unit cell: (135.29, 118.69, 32.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     822      8.00
     N     708      7.00
     C    2574      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 176.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1008

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 44.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 9
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 18
      removed outlier: 7.018A  pdb=" N   GLU A  13 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   VAL B  16 " --> pdb=" O   GLU A  13 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   ALA B  18 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA A  17 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLU B  13 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   VAL C  16 " --> pdb=" O   GLU B  13 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   VAL B  15 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ALA C  18 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ALA B  17 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 29
      removed outlier: 6.908A  pdb=" N   GLY A  25 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   GLY B  25 " --> pdb=" O   GLN C  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 40
      removed outlier: 6.373A  pdb=" N   LYS A  34 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   VAL B  37 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   GLY A  36 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 9.902A  pdb=" N   TYR B  39 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 8.655A  pdb=" N   LEU A  38 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS B  34 " --> pdb=" O   GLU C  35 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   VAL C  37 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   GLY B  36 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   TYR C  39 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 8.672A  pdb=" N   LEU B  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 52
      removed outlier: 7.030A  pdb=" N   GLY A  47 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   HIS B  50 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL B  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLY A  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLY B  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   HIS C  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   VAL B  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   VAL C  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   GLY B  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 63 through 67
    Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 71
    Processing sheet with id=AA8, first strand: chain 'A' and resid 74 through 78
    Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 95
      removed outlier: 6.332A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   THR B  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ALA A  91 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   PHE B  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   GLY A  93 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ALA B  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 8.192A  pdb=" N   THR C  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA B  91 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 8.627A  pdb=" N   PHE C  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 8.847A  pdb=" N   GLY B  93 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 9
    Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 18
      removed outlier: 7.016A  pdb=" N   GLU F  13 " --> pdb=" O   GLY G  14 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   VAL G  16 " --> pdb=" O   GLU F  13 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   VAL F  15 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ALA G  18 " --> pdb=" O   VAL F  15 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA F  17 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   GLU G  13 " --> pdb=" O   GLY H  14 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   VAL H  16 " --> pdb=" O   GLU G  13 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   VAL G  15 " --> pdb=" O   VAL H  16 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   ALA H  18 " --> pdb=" O   VAL G  15 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ALA G  17 " --> pdb=" O   ALA H  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'F' and resid 24 through 29
      removed outlier: 6.908A  pdb=" N   GLY F  25 " --> pdb=" O   GLN G  24 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLY G  25 " --> pdb=" O   GLN H  24 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 34 through 40
      removed outlier: 6.374A  pdb=" N   LYS F  34 " --> pdb=" O   GLU G  35 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   VAL G  37 " --> pdb=" O   LYS F  34 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   GLY F  36 " --> pdb=" O   VAL G  37 " (cutoff:3.500A)
      removed outlier: 9.903A  pdb=" N   TYR G  39 " --> pdb=" O   GLY F  36 " (cutoff:3.500A)
      removed outlier: 8.656A  pdb=" N   LEU F  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LYS G  34 " --> pdb=" O   GLU H  35 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   VAL H  37 " --> pdb=" O   LYS G  34 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   GLY G  36 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 9.927A  pdb=" N   TYR H  39 " --> pdb=" O   GLY G  36 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   LEU G  38 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'F' and resid 46 through 52
      removed outlier: 7.030A  pdb=" N   GLY F  47 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   HIS G  50 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   VAL F  49 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL G  52 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   GLY F  51 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   GLY G  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   HIS H  50 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   VAL G  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   VAL H  52 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   GLY G  51 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 67
    Processing sheet with id=AB7, first strand: chain 'F' and resid 70 through 71
    Processing sheet with id=AB8, first strand: chain 'F' and resid 74 through 78
    Processing sheet with id=AB9, first strand: chain 'F' and resid 88 through 95
      removed outlier: 6.332A  pdb=" N   ALA F  89 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   THR G  92 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ALA F  91 " --> pdb=" O   THR G  92 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   PHE G  94 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
      removed outlier: 8.827A  pdb=" N   GLY F  93 " --> pdb=" O   PHE G  94 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ALA G  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   THR H  92 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ALA G  91 " --> pdb=" O   THR H  92 " (cutoff:3.500A)
      removed outlier: 8.636A  pdb=" N   PHE H  94 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   GLY G  93 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    72 hydrogen bonds defined for protein.
    216 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1362
        1.34 -     1.45: 314
        1.45 -     1.57: 2434
        1.57 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 4134
  Sorted by residual:
  bond pdb=" C   ACE A   0 "
       pdb=" O   ACE A   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.228 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C   ACE G   0 "
       pdb=" O   ACE G   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.228 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C   ACE F   0 "
       pdb=" O   ACE F   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.227 -0.028 2.00e-02 2.50e+03 2.03e+00
  bond pdb=" C   ACE H   0 "
       pdb=" O   ACE H   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.227 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C   ACE C   0 "
       pdb=" O   ACE C   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.227 -0.028 2.00e-02 2.50e+03 1.89e+00
  ... (remaining 4129 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.69: 4726
        0.69 -     1.39: 676
        1.39 -     2.08: 87
        2.08 -     2.77: 49
        2.77 -     3.46: 6
  Bond angle restraints: 5544
  Sorted by residual:
  angle pdb=" CA  GLY G   7 "
        pdb=" C   GLY G   7 "
        pdb=" N   LEU G   8 "
      ideal   model   delta    sigma   weight residual
     115.31  117.60   -2.29 1.28e+00 6.10e-01 3.21e+00
  angle pdb=" CA  GLY B   7 "
        pdb=" C   GLY B   7 "
        pdb=" N   LEU B   8 "
      ideal   model   delta    sigma   weight residual
     115.31  117.55   -2.24 1.28e+00 6.10e-01 3.05e+00
  angle pdb=" CA  GLY A   7 "
        pdb=" C   GLY A   7 "
        pdb=" N   LEU A   8 "
      ideal   model   delta    sigma   weight residual
     115.31  117.52   -2.21 1.28e+00 6.10e-01 2.99e+00
  angle pdb=" CA  GLY C   7 "
        pdb=" C   GLY C   7 "
        pdb=" N   LEU C   8 "
      ideal   model   delta    sigma   weight residual
     115.31  117.52   -2.21 1.28e+00 6.10e-01 2.97e+00
  angle pdb=" N   GLY G   7 "
        pdb=" CA  GLY G   7 "
        pdb=" C   GLY G   7 "
      ideal   model   delta    sigma   weight residual
     110.20  112.47   -2.27 1.32e+00 5.74e-01 2.97e+00
  ... (remaining 5539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 2358
       17.82 -    35.63: 90
       35.63 -    53.45: 30
       53.45 -    71.27: 0
       71.27 -    89.08: 6
  Dihedral angle restraints: 2484
    sinusoidal: 888
      harmonic: 1596
  Sorted by residual:
  dihedral pdb=" CA  GLU G  83 "
           pdb=" C   GLU G  83 "
           pdb=" N   GLY G  84 "
           pdb=" CA  GLY G  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.70   18.30     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  GLU C  83 "
           pdb=" C   GLU C  83 "
           pdb=" N   GLY C  84 "
           pdb=" CA  GLY C  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  GLU B  83 "
           pdb=" C   GLU B  83 "
           pdb=" N   GLY B  84 "
           pdb=" CA  GLY B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.74   18.26     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 2481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 386
       0.034 -    0.068: 188
       0.068 -    0.103: 68
       0.103 -    0.137: 42
       0.137 -    0.171: 6
  Chirality restraints: 690
  Sorted by residual:
  chirality pdb=" CG  LEU C   8 "
            pdb=" CB  LEU C   8 "
            pdb=" CD1 LEU C   8 "
            pdb=" CD2 LEU C   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.32e-01
  chirality pdb=" CG  LEU G   8 "
            pdb=" CB  LEU G   8 "
            pdb=" CD1 LEU G   8 "
            pdb=" CD2 LEU G   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CG  LEU F   8 "
            pdb=" CB  LEU F   8 "
            pdb=" CD1 LEU F   8 "
            pdb=" CD2 LEU F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 6.99e-01
  ... (remaining 687 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H  48 "    0.002 2.00e-02 2.50e+03   4.75e-03 2.26e-01
        pdb=" C   VAL H  48 "   -0.008 2.00e-02 2.50e+03
        pdb=" O   VAL H  48 "    0.003 2.00e-02 2.50e+03
        pdb=" N   VAL H  49 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F  67 "   -0.002 2.00e-02 2.50e+03   4.73e-03 2.24e-01
        pdb=" C   GLY F  67 "    0.008 2.00e-02 2.50e+03
        pdb=" O   GLY F  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   GLY F  68 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  48 "   -0.002 2.00e-02 2.50e+03   4.62e-03 2.14e-01
        pdb=" C   VAL A  48 "    0.008 2.00e-02 2.50e+03
        pdb=" O   VAL A  48 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   VAL A  49 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1429
        2.87 -     3.38: 3320
        3.38 -     3.89: 6207
        3.89 -     4.39: 6611
        4.39 -     4.90: 13776
  Nonbonded interactions: 31343
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B   2 "
            pdb=" NZ  LYS B  10 "
     model   vdw
     2.368 3.120
  nonbonded pdb=" OD2 ASP G   2 "
            pdb=" NZ  LYS G  10 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OD2 ASP A   2 "
            pdb=" NZ  LYS A  10 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OD2 ASP H   2 "
            pdb=" NZ  LYS H  10 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OD2 ASP C   2 "
            pdb=" NZ  LYS C  10 "
     model   vdw
     2.369 3.120
  ... (remaining 31338 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 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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 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:             2.860
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     5.690
  Find NCS groups from input model:        0.050
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
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      :  0.007   0.029   4134  Z= 0.323
  Angle     :  0.545   3.463   5544  Z= 0.326
  Chirality :  0.052   0.171    690
  Planarity :  0.001   0.005    696
  Dihedral  : 12.258  89.081   1476
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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: -4.52 (0.23), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.17), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR F  39 
 PHE   0.006   0.001   PHE G   4 
 HIS   0.003   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00709 ( 4134)
  covalent geometry    : angle       0.54549 ( 5544)
  hydrogen bonds       : bond        0.21611 (   72)
  hydrogen bonds       : angle       8.36055 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.160 
Fit side-chains
REVERT: C   34 LYS cc_start: 0.8821 (mttt) cc_final: 0.8611 (mttm)
REVERT: F   21 LYS cc_start: 0.8738 (mttm) cc_final: 0.8254 (mtmt)
REVERT: F   57 GLU cc_start: 0.8083 (tt0) cc_final: 0.7776 (tm-30)
REVERT: F   96 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7424 (mttm)
REVERT: F   97 LYS cc_start: 0.7477 (ptpt) cc_final: 0.7100 (tttp)
REVERT: G   96 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7738 (mttm)
REVERT: G   97 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6666 (tttt)
REVERT: H   20 GLU cc_start: 0.8606 (tp30) cc_final: 0.8299 (mm-30)
REVERT: H   21 LYS cc_start: 0.8762 (mttm) cc_final: 0.8471 (mttt)
REVERT: H   96 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7908 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0687
  time to fit residues: 8.2567
Evaluate side-chains
  78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
C  50 HIS
F  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.094405 restraints weight = 5638.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.096830 restraints weight = 2673.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.098350 restraints weight = 1605.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.099461 restraints weight = 1117.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.100193 restraints weight = 846.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4134  Z= 0.108
  Angle     :  0.446   3.202   5544  Z= 0.257
  Chirality :  0.050   0.129    690
  Planarity :  0.002   0.009    696
  Dihedral  :  5.001  16.790    600
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.97 %
    Favored  : 84.80 %
  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: -3.70 (0.27), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.20), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  39 
 PHE   0.005   0.001   PHE C   4 
 HIS   0.005   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4134)
  covalent geometry    : angle       0.44650 ( 5544)
  hydrogen bonds       : bond        0.02914 (   72)
  hydrogen bonds       : angle       4.61097 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: F   21 LYS cc_start: 0.8714 (mttm) cc_final: 0.8295 (mtmt)
REVERT: F   97 LYS cc_start: 0.7116 (ptpt) cc_final: 0.6830 (pttm)
REVERT: G   57 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7232 (tm-30)
REVERT: G   96 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7635 (mttm)
REVERT: H   20 GLU cc_start: 0.8325 (tp30) cc_final: 0.8000 (mm-30)
REVERT: H   21 LYS cc_start: 0.8642 (mttm) cc_final: 0.7478 (mmtt)
REVERT: H   96 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7820 (tptt)
  outliers start: 5
  outliers final: 4
  residues processed: 87
  average time/residue: 0.0630
  time to fit residues: 6.9877
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    8.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.095791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085586 restraints weight = 5937.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.087760 restraints weight = 2803.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089217 restraints weight = 1696.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.090210 restraints weight = 1188.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.090896 restraints weight = 909.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.056   4134  Z= 0.505
  Angle     :  0.718   5.389   5544  Z= 0.403
  Chirality :  0.056   0.127    690
  Planarity :  0.003   0.009    696
  Dihedral  :  5.997  24.090    600
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 12.01 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.85 (0.26), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.20), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR B  39 
 PHE   0.007   0.001   PHE C  94 
 HIS   0.005   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01172 ( 4134)
  covalent geometry    : angle       0.71802 ( 5544)
  hydrogen bonds       : bond        0.04093 (   72)
  hydrogen bonds       : angle       4.90409 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8626 (mp0) cc_final: 0.7925 (mp0)
REVERT: F   20 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8437 (mm-30)
REVERT: F   21 LYS cc_start: 0.8777 (mttm) cc_final: 0.8188 (mtmt)
REVERT: F   57 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: F   97 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6851 (pttm)
REVERT: G   57 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: G   58 LYS cc_start: 0.9224 (mttt) cc_final: 0.8394 (mttp)
REVERT: G   96 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7667 (mttm)
REVERT: H   97 LYS cc_start: 0.4861 (mmmt) cc_final: 0.4660 (mmmt)
  outliers start: 27
  outliers final: 21
  residues processed: 99
  average time/residue: 0.0559
  time to fit residues: 7.2763
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   64 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   83 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.104868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.094999 restraints weight = 5672.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.097315 restraints weight = 2615.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.098841 restraints weight = 1545.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.099903 restraints weight = 1049.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.100586 restraints weight = 783.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4134  Z= 0.102
  Angle     :  0.453   3.603   5544  Z= 0.258
  Chirality :  0.050   0.132    690
  Planarity :  0.001   0.009    696
  Dihedral  :  5.233  18.032    600
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.65 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.41 (0.28), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR B  39 
 PHE   0.021   0.001   PHE A   4 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4134)
  covalent geometry    : angle       0.45297 ( 5544)
  hydrogen bonds       : bond        0.02367 (   72)
  hydrogen bonds       : angle       4.25914 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C    5 MET cc_start: 0.8312 (mmt) cc_final: 0.8111 (mmt)
REVERT: F   13 GLU cc_start: 0.8531 (mp0) cc_final: 0.7988 (mp0)
REVERT: F   21 LYS cc_start: 0.8765 (mttm) cc_final: 0.8276 (mtmt)
REVERT: F   97 LYS cc_start: 0.7238 (ptpt) cc_final: 0.6941 (pttm)
REVERT: G   58 LYS cc_start: 0.9159 (mttt) cc_final: 0.8905 (mttp)
REVERT: H   21 LYS cc_start: 0.8705 (mttm) cc_final: 0.7432 (mmtt)
REVERT: H   58 LYS cc_start: 0.9012 (mttt) cc_final: 0.8651 (mttp)
  outliers start: 9
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0626
  time to fit residues: 6.7066
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.108049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.098122 restraints weight = 5559.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.100497 restraints weight = 2567.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.102069 restraints weight = 1509.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.103101 restraints weight = 1021.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103805 restraints weight = 762.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   4134  Z= 0.091
  Angle     :  0.422   3.322   5544  Z= 0.241
  Chirality :  0.050   0.129    690
  Planarity :  0.001   0.007    696
  Dihedral  :  4.848  17.909    600
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.91 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.16 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.014   0.001   PHE A   4 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 4134)
  covalent geometry    : angle       0.42198 ( 5544)
  hydrogen bonds       : bond        0.02149 (   72)
  hydrogen bonds       : angle       4.04308 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: C    5 MET cc_start: 0.8273 (mmt) cc_final: 0.8073 (mmt)
REVERT: F   13 GLU cc_start: 0.8533 (mp0) cc_final: 0.8011 (mp0)
REVERT: F   21 LYS cc_start: 0.8741 (mttm) cc_final: 0.8268 (mtmt)
REVERT: F   97 LYS cc_start: 0.7188 (ptpt) cc_final: 0.6854 (pttm)
REVERT: G   58 LYS cc_start: 0.9197 (mttt) cc_final: 0.8905 (mttp)
  outliers start: 12
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0646
  time to fit residues: 6.8509
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0570
   chunk 8 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   overall best weight:    3.2106

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.104651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095174 restraints weight = 5803.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.097544 restraints weight = 2575.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.099062 restraints weight = 1473.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.100094 restraints weight = 978.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.100785 restraints weight = 720.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4134  Z= 0.188
  Angle     :  0.479   4.149   5544  Z= 0.271
  Chirality :  0.050   0.127    690
  Planarity :  0.001   0.007    696
  Dihedral  :  5.067  17.988    600
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 15.93 %
    Favored  : 80.39 %
  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: -3.17 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  39 
 PHE   0.009   0.001   PHE A   4 
 HIS   0.007   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4134)
  covalent geometry    : angle       0.47910 ( 5544)
  hydrogen bonds       : bond        0.02399 (   72)
  hydrogen bonds       : angle       4.28743 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: F   20 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8612 (mm-30)
REVERT: F   21 LYS cc_start: 0.8766 (mttm) cc_final: 0.8201 (mtmt)
REVERT: F   97 LYS cc_start: 0.7269 (ptpt) cc_final: 0.6881 (pttm)
REVERT: G   58 LYS cc_start: 0.9220 (mttt) cc_final: 0.8981 (mttp)
  outliers start: 15
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0545
  time to fit residues: 5.9761
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 12 optimal weight:    0.1980
   chunk 49 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 19 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0670
   overall best weight:    1.1520

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.110509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101093 restraints weight = 5650.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.103569 restraints weight = 2514.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.105100 restraints weight = 1426.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.106146 restraints weight = 943.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.106835 restraints weight = 686.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   4134  Z= 0.081
  Angle     :  0.417   3.159   5544  Z= 0.237
  Chirality :  0.050   0.130    690
  Planarity :  0.001   0.006    696
  Dihedral  :  4.753  16.199    600
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 16.42 %
    Favored  : 79.66 %
  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: -2.99 (0.31), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  39 
 PHE   0.010   0.001   PHE A   4 
 HIS   0.006   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 4134)
  covalent geometry    : angle       0.41655 ( 5544)
  hydrogen bonds       : bond        0.02083 (   72)
  hydrogen bonds       : angle       3.96284 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8549 (mp0) cc_final: 0.7966 (mp0)
REVERT: F   21 LYS cc_start: 0.8744 (mttm) cc_final: 0.8244 (mtmt)
REVERT: F   97 LYS cc_start: 0.7214 (ptpt) cc_final: 0.6821 (pttm)
REVERT: G   58 LYS cc_start: 0.9184 (mttt) cc_final: 0.8941 (mttp)
  outliers start: 16
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0600
  time to fit residues: 6.2779
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.099944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.090412 restraints weight = 5829.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092722 restraints weight = 2684.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.094207 restraints weight = 1566.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.095125 restraints weight = 1052.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.095818 restraints weight = 794.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.052   4134  Z= 0.394
  Angle     :  0.629   5.820   5544  Z= 0.353
  Chirality :  0.053   0.143    690
  Planarity :  0.002   0.007    696
  Dihedral  :  5.634  21.547    600
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.16 %
    Favored  : 79.17 %
  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: -3.23 (0.29), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR B  39 
 PHE   0.007   0.002   PHE B   4 
 HIS   0.006   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00914 ( 4134)
  covalent geometry    : angle       0.62870 ( 5544)
  hydrogen bonds       : bond        0.02976 (   72)
  hydrogen bonds       : angle       4.60013 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8620 (mp0) cc_final: 0.7868 (mp0)
REVERT: F   20 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8487 (mm-30)
REVERT: F   21 LYS cc_start: 0.8784 (mttm) cc_final: 0.8178 (mtmt)
REVERT: F   57 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: F   97 LYS cc_start: 0.7208 (ptpt) cc_final: 0.6888 (pttm)
REVERT: G   58 LYS cc_start: 0.9235 (mttt) cc_final: 0.9030 (mttp)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.0573
  time to fit residues: 6.2980
Evaluate side-chains
  86 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  50 HIS
H  50 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.107656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.098172 restraints weight = 5666.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.100645 restraints weight = 2498.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102216 restraints weight = 1409.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103230 restraints weight = 921.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.103909 restraints weight = 674.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4134  Z= 0.116
  Angle     :  0.457   4.543   5544  Z= 0.260
  Chirality :  0.051   0.132    690
  Planarity :  0.001   0.008    696
  Dihedral  :  5.075  18.322    600
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.40 %
    Favored  : 79.66 %
  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: -3.03 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR A  39 
 PHE   0.013   0.001   PHE B   4 
 HIS   0.010   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4134)
  covalent geometry    : angle       0.45669 ( 5544)
  hydrogen bonds       : bond        0.02223 (   72)
  hydrogen bonds       : angle       4.13340 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8527 (mp0) cc_final: 0.7913 (mp0)
REVERT: F   20 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8699 (mm-30)
REVERT: F   21 LYS cc_start: 0.8761 (mttm) cc_final: 0.8190 (mtmt)
REVERT: F   97 LYS cc_start: 0.7279 (ptpt) cc_final: 0.6914 (pttm)
REVERT: G   58 LYS cc_start: 0.9200 (mttt) cc_final: 0.8927 (mttp)
REVERT: H   50 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7165 (t-90)
  outliers start: 12
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0567
  time to fit residues: 5.9927
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   64 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  50 HIS
H  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.105649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.096066 restraints weight = 5698.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.098514 restraints weight = 2528.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.100051 restraints weight = 1439.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.101040 restraints weight = 951.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101733 restraints weight = 703.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4134  Z= 0.189
  Angle     :  0.489   4.825   5544  Z= 0.278
  Chirality :  0.050   0.136    690
  Planarity :  0.002   0.011    696
  Dihedral  :  5.085  18.618    600
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.16 %
    Favored  : 79.90 %
  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: -3.01 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  39 
 PHE   0.017   0.002   PHE F   4 
 HIS   0.014   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 4134)
  covalent geometry    : angle       0.48918 ( 5544)
  hydrogen bonds       : bond        0.02292 (   72)
  hydrogen bonds       : angle       4.26381 (  216)

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8554 (mp0) cc_final: 0.7894 (mp0)
REVERT: F   20 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: F   21 LYS cc_start: 0.8785 (mttm) cc_final: 0.8190 (mtmt)
REVERT: F   97 LYS cc_start: 0.7189 (ptpt) cc_final: 0.6877 (pttm)
  outliers start: 12
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0563
  time to fit residues: 5.6320
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain F residue    2 ASP
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 42 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    5.2588

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.101780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.092226 restraints weight = 5825.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.094578 restraints weight = 2657.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.096085 restraints weight = 1536.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.097020 restraints weight = 1025.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.097735 restraints weight = 768.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   4134  Z= 0.301
  Angle     :  0.571   5.306   5544  Z= 0.322
  Chirality :  0.052   0.127    690
  Planarity :  0.002   0.007    696
  Dihedral  :  5.509  20.130    600
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.16 %
    Favored  : 79.41 %
  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: -3.13 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  39 
 PHE   0.014   0.002   PHE F   4 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 ( 4134)
  covalent geometry    : angle       0.57101 ( 5544)
  hydrogen bonds       : bond        0.02678 (   72)
  hydrogen bonds       : angle       4.51104 (  216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 825.10 seconds
wall clock time: 14 minutes 55.51 seconds (895.51 seconds total)