Starting phenix.real_space_refine
on Wed Mar  5 23:38:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zlp_60232/03_2025/8zlp_60232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zlp_60232/03_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_60232/03_2025/8zlp_60232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zlp_60232/03_2025/8zlp_60232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zlp_60232/03_2025/8zlp_60232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zlp_60232/03_2025/8zlp_60232.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, G, F, H
  Time building chain proxies: 2.90, per 1000 atoms: 0.70
  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: 1.03
  Conformation dependent library (CDL) restraints added in 567.1 milliseconds
  

  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: 0.52
  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: 0.94

  Time building geometry restraints manager: 1.23 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'G'
  selection = chain 'F'
  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:             2.830
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.380
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.480
-------------------------------------------------------------------------------
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= 0.480
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.003   0.002   HIS G  50 
 PHE   0.006   0.001   PHE G   4 
 TYR   0.005   0.002   TYR F  39 

*********************** 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  : 0.483 
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: 0.8256 (mtmt)
REVERT: F   96 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7425 (mttm)
REVERT: F   97 LYS cc_start: 0.7477 (ptpt) cc_final: 0.7101 (tttp)
REVERT: G   57 GLU cc_start: 0.7905 (tt0) cc_final: 0.7505 (tm-30)
REVERT: G   96 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7740 (mttm)
REVERT: G   97 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6667 (tttt)
REVERT: H   20 GLU cc_start: 0.8606 (tp30) cc_final: 0.8301 (mm-30)
REVERT: H   21 LYS cc_start: 0.8762 (mttm) cc_final: 0.8468 (mttt)
REVERT: H   96 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7909 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1590
  time to fit residues: 19.0519
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  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.105690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.095337 restraints weight = 5478.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.097731 restraints weight = 2553.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.099303 restraints weight = 1516.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4134  Z= 0.153
  Angle     :  0.447   3.211   5544  Z= 0.257
  Chirality :  0.050   0.131    690
  Planarity :  0.002   0.009    696
  Dihedral  :  4.983  16.506    600
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.24 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.005   0.002   HIS C  50 
 PHE   0.005   0.001   PHE C   4 
 TYR   0.007   0.001   TYR A  39 

*********************** 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
  91 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: F   21 LYS cc_start: 0.8739 (mttm) cc_final: 0.8291 (mtmt)
REVERT: F   97 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6840 (pttm)
REVERT: G   79 GLN cc_start: 0.9264 (mt0) cc_final: 0.8872 (mt0)
REVERT: G   96 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7602 (mttm)
REVERT: H   20 GLU cc_start: 0.8333 (tp30) cc_final: 0.7982 (mm-30)
REVERT: H   21 LYS cc_start: 0.8653 (mttm) cc_final: 0.7479 (mmtt)
REVERT: H   96 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7809 (tptt)
  outliers start: 5
  outliers final: 4
  residues processed: 87
  average time/residue: 0.1667
  time to fit residues: 18.1740
Evaluate side-chains
  86 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
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 35 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.099497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.089307 restraints weight = 5714.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.091518 restraints weight = 2693.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.093043 restraints weight = 1626.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   4134  Z= 0.500
  Angle     :  0.564   3.750   5544  Z= 0.318
  Chirality :  0.051   0.122    690
  Planarity :  0.002   0.008    696
  Dihedral  :  5.449  20.596    600
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 12.99 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.27), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.21), residues: 576

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

*********************** 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
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8587 (mp0) cc_final: 0.7976 (mp0)
REVERT: F   20 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8567 (mm-30)
REVERT: F   21 LYS cc_start: 0.8777 (mttm) cc_final: 0.8230 (mtmt)
REVERT: F   57 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: F   97 LYS cc_start: 0.7312 (ptpt) cc_final: 0.6972 (pttm)
REVERT: G   57 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: G   58 LYS cc_start: 0.9156 (mttt) cc_final: 0.8319 (mttp)
REVERT: G   96 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7621 (mttm)
REVERT: H   21 LYS cc_start: 0.8724 (mttm) cc_final: 0.7587 (mmtt)
REVERT: H   96 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7976 (tptt)
REVERT: H   97 LYS cc_start: 0.4922 (mmmt) cc_final: 0.4697 (mmmt)
  outliers start: 18
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1508
  time to fit residues: 17.1848
Evaluate side-chains
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   64 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
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 40 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.106143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.096008 restraints weight = 5634.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.098363 restraints weight = 2621.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.099935 restraints weight = 1554.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   4134  Z= 0.143
  Angle     :  0.424   3.245   5544  Z= 0.243
  Chirality :  0.050   0.131    690
  Planarity :  0.001   0.007    696
  Dihedral  :  4.977  16.093    600
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.29), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.22), residues: 576

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

*********************** 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
  88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8547 (mp0) cc_final: 0.8049 (mp0)
REVERT: F   21 LYS cc_start: 0.8732 (mttm) cc_final: 0.8285 (mtmt)
REVERT: F   97 LYS cc_start: 0.7173 (ptpt) cc_final: 0.6856 (pttm)
REVERT: G   58 LYS cc_start: 0.9149 (mttt) cc_final: 0.8839 (mttp)
REVERT: G   79 GLN cc_start: 0.9258 (mt0) cc_final: 0.8871 (mt0)
REVERT: G   96 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7604 (mttm)
REVERT: H   20 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: H   21 LYS cc_start: 0.8717 (mttm) cc_final: 0.7458 (mmtt)
REVERT: H   96 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7932 (tptt)
REVERT: H   97 LYS cc_start: 0.4895 (mmmt) cc_final: 0.4608 (mmmt)
  outliers start: 11
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1647
  time to fit residues: 18.0766
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain F residue   44 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 34 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.099901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.089793 restraints weight = 5869.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.092088 restraints weight = 2705.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.093650 restraints weight = 1604.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4134  Z= 0.423
  Angle     :  0.530   4.016   5544  Z= 0.300
  Chirality :  0.051   0.126    690
  Planarity :  0.002   0.010    696
  Dihedral  :  5.342  19.763    600
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 14.22 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.29), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS H  50 
 PHE   0.022   0.002   PHE A   4 
 TYR   0.008   0.002   TYR B  39 

*********************** 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
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8571 (mp0) cc_final: 0.7937 (mp0)
REVERT: F   20 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8549 (mm-30)
REVERT: F   21 LYS cc_start: 0.8766 (mttm) cc_final: 0.8208 (mtmt)
REVERT: F   57 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7497 (tm-30)
REVERT: F   97 LYS cc_start: 0.7249 (ptpt) cc_final: 0.6823 (pttm)
REVERT: G   58 LYS cc_start: 0.9216 (mttt) cc_final: 0.8923 (mttp)
REVERT: G   96 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7638 (mttm)
REVERT: H   21 LYS cc_start: 0.8779 (mttm) cc_final: 0.7567 (mmtt)
REVERT: H   57 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7602 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1412
  time to fit residues: 15.5747
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 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   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   46 GLU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 44 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.100377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090343 restraints weight = 5746.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.092622 restraints weight = 2677.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.094152 restraints weight = 1595.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   4134  Z= 0.380
  Angle     :  0.516   3.809   5544  Z= 0.292
  Chirality :  0.051   0.129    690
  Planarity :  0.002   0.007    696
  Dihedral  :  5.393  20.629    600
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 14.95 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.29), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.014   0.001   PHE A   4 
 TYR   0.008   0.002   TYR B  39 

*********************** 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
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8563 (mp0) cc_final: 0.7927 (mp0)
REVERT: F   20 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: F   21 LYS cc_start: 0.8758 (mttm) cc_final: 0.8200 (mtmt)
REVERT: F   57 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: F   97 LYS cc_start: 0.7205 (ptpt) cc_final: 0.6818 (pttm)
REVERT: G   58 LYS cc_start: 0.9233 (mttt) cc_final: 0.9002 (mttp)
REVERT: H   57 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7518 (tm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1270
  time to fit residues: 14.0145
Evaluate side-chains
  91 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 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 G residue   44 THR
Chi-restraints excluded: chain G residue   46 GLU
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   46 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.101539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.091695 restraints weight = 5719.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.094033 restraints weight = 2617.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.095573 restraints weight = 1528.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4134  Z= 0.364
  Angle     :  0.510   3.980   5544  Z= 0.289
  Chirality :  0.051   0.128    690
  Planarity :  0.002   0.007    696
  Dihedral  :  5.379  19.872    600
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.29), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  50 
 PHE   0.011   0.001   PHE A   4 
 TYR   0.007   0.002   TYR B  39 

*********************** 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
  90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8564 (mp0) cc_final: 0.7915 (mp0)
REVERT: F   20 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8542 (mm-30)
REVERT: F   21 LYS cc_start: 0.8751 (mttm) cc_final: 0.8169 (mtmt)
REVERT: F   57 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7485 (tm-30)
REVERT: F   97 LYS cc_start: 0.7209 (ptpt) cc_final: 0.6847 (pttm)
REVERT: G   58 LYS cc_start: 0.9236 (mttt) cc_final: 0.9014 (mttp)
REVERT: H   57 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7521 (tm-30)
  outliers start: 16
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1373
  time to fit residues: 14.7599
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   59 THR
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   42 SER
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   46 GLU
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   46 GLU
Chi-restraints excluded: chain H residue   48 VAL
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 45 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0270
   chunk 43 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0770
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.3400

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.108447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.098807 restraints weight = 5581.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.101257 restraints weight = 2506.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.102771 restraints weight = 1430.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2346

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= 0.137
  Angle     :  0.423   3.181   5544  Z= 0.242
  Chirality :  0.050   0.131    690
  Planarity :  0.001   0.007    696
  Dihedral  :  4.901  16.395    600
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.31), 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
 HIS   0.003   0.000   HIS A  50 
 PHE   0.010   0.001   PHE A   4 
 TYR   0.005   0.001   TYR A  39 

*********************** 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
  86 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8523 (mp0) cc_final: 0.7992 (mp0)
REVERT: F   21 LYS cc_start: 0.8723 (mttm) cc_final: 0.8260 (mtmt)
REVERT: F   97 LYS cc_start: 0.7208 (ptpt) cc_final: 0.6791 (pttm)
REVERT: G   58 LYS cc_start: 0.9216 (mttt) cc_final: 0.8981 (mttp)
REVERT: H   57 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7383 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1358
  time to fit residues: 14.3995
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 G residue   46 GLU
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0970
   overall best weight:    2.6186

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.105078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.095398 restraints weight = 5705.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.097784 restraints weight = 2550.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.099341 restraints weight = 1467.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4134  Z= 0.251
  Angle     :  0.463   3.582   5544  Z= 0.263
  Chirality :  0.050   0.127    690
  Planarity :  0.001   0.010    696
  Dihedral  :  4.995  20.585    600
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS H  50 
 PHE   0.022   0.002   PHE B   4 
 TYR   0.005   0.001   TYR B  39 

*********************** 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
  85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8527 (mp0) cc_final: 0.7935 (mp0)
REVERT: F   20 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8627 (mm-30)
REVERT: F   21 LYS cc_start: 0.8772 (mttm) cc_final: 0.8190 (mtmt)
REVERT: F   97 LYS cc_start: 0.7240 (ptpt) cc_final: 0.6824 (pttm)
REVERT: G   58 LYS cc_start: 0.9221 (mttt) cc_final: 0.8990 (mttp)
  outliers start: 12
  outliers final: 12
  residues processed: 78
  average time/residue: 0.1425
  time to fit residues: 14.3415
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  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
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   44 THR
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0870
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    3.3364

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.103347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.093707 restraints weight = 5652.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.096059 restraints weight = 2537.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.097531 restraints weight = 1458.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4134  Z= 0.310
  Angle     :  0.492   3.789   5544  Z= 0.279
  Chirality :  0.050   0.127    690
  Planarity :  0.002   0.009    696
  Dihedral  :  5.191  21.029    600
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.30), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS H  50 
 PHE   0.020   0.002   PHE B   4 
 TYR   0.006   0.001   TYR B  39 

********************** 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
  88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: F   13 GLU cc_start: 0.8517 (mp0) cc_final: 0.7916 (mp0)
REVERT: F   21 LYS cc_start: 0.8754 (mttm) cc_final: 0.8251 (mtmt)
REVERT: F   57 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: F   97 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6819 (pttm)
REVERT: G    5 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7267 (mmm)
REVERT: G   58 LYS cc_start: 0.9220 (mttt) cc_final: 0.9003 (mttp)
  outliers start: 13
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1508
  time to fit residues: 15.4509
Evaluate side-chains
  88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain B residue   81 THR
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    5 MET
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 27 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 14 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
** H  50 HIS ** 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 = 0.3570 r_free = 0.3570 target = 0.109149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.099621 restraints weight = 5605.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.102079 restraints weight = 2503.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.103625 restraints weight = 1424.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4134  Z= 0.142
  Angle     :  0.423   3.087   5544  Z= 0.243
  Chirality :  0.050   0.130    690
  Planarity :  0.001   0.009    696
  Dihedral  :  4.815  18.197    600
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.31), residues: 576
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS H  50 
 PHE   0.019   0.002   PHE B   4 
 TYR   0.004   0.001   TYR B  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1571.71 seconds
wall clock time: 28 minutes 17.05 seconds (1697.05 seconds total)