Starting phenix.real_space_refine
on Tue Mar  3 12:06:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ozh_13124/03_2026/7ozh_13124.cif"
  }
  resolution = 3.02
  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=   1.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2410      2.51       5
     N     680      2.21       5
     O     800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3890
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 389
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Residues with excluded nonbonded symmetry interactions: 10
    residue:
      pdb=" N   LYS A  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS A  45 " occ=0.50
    residue:
      pdb=" N   LYS B  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS B  45 " occ=0.50
    residue:
      pdb=" N   LYS C  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS C  45 " occ=0.50
    residue:
      pdb=" N   LYS D  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS D  45 " occ=0.50
    residue:
      pdb=" N   LYS E  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS E  45 " occ=0.50
    residue:
      pdb=" N   LYS F  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS F  45 " occ=0.50
    residue:
      pdb=" N   LYS G  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS G  45 " occ=0.50
    residue:
      pdb=" N   LYS H  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS H  45 " occ=0.50
    residue:
      pdb=" N   LYS I  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS I  45 " occ=0.50
    residue:
      pdb=" N   LYS J  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS J  45 " occ=0.50
  Time building chain proxies: 0.39, per 1000 atoms: 0.10
  Number of scatterers: 3890
  At special positions: 0
  Unit cell: (116.55, 76.65, 43.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     800      8.00
     N     680      7.00
     C    2410      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: 0.32
  Conformation dependent library (CDL) restraints added in 205.1 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42
      removed outlier: 6.247A  pdb=" N   GLY A  41 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY C  41 " --> pdb=" O   SER E  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY E  41 " --> pdb=" O   SER G  42 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLY G  41 " --> pdb=" O   SER I  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.507A  pdb=" N   VAL A  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL E  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL G  48 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76
      removed outlier: 6.845A  pdb=" N   THR A  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ALA C  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR C  75 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA E  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR E  75 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA G  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR G  75 " --> pdb=" O   VAL I  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA I  76 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.404A  pdb=" N   ILE A  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE C  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE E  88 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE G  88 " --> pdb=" O   ALA I  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42
      removed outlier: 6.246A  pdb=" N   GLY B  41 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY D  41 " --> pdb=" O   SER F  42 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLY F  41 " --> pdb=" O   SER H  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY H  41 " --> pdb=" O   SER J  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49
      removed outlier: 6.509A  pdb=" N   VAL B  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL D  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL F  48 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL H  48 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66
    Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 76
      removed outlier: 6.846A  pdb=" N   THR B  75 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA D  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR D  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA F  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR F  75 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA H  76 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR H  75 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA J  76 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89
      removed outlier: 6.404A  pdb=" N   ILE B  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ILE D  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE F  88 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE H  88 " --> pdb=" O   ALA J  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    56 hydrogen bonds defined for protein.
    168 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: 0.42

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.20 -     1.28: 690
        1.28 -     1.35: 630
        1.35 -     1.43: 269
        1.43 -     1.51: 1434
        1.51 -     1.58: 877
  Bond restraints: 3900
  Sorted by residual:
  bond pdb=" CA  LYS D  45 "
       pdb=" CB  LYS D  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.95e+01
  bond pdb=" CA  LYS H  45 "
       pdb=" CB  LYS H  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.94e+01
  bond pdb=" CA  LYS E  45 "
       pdb=" CB  LYS E  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  bond pdb=" CA  LYS J  45 "
       pdb=" CB  LYS J  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  bond pdb=" CA  LYS G  45 "
       pdb=" CB  LYS G  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  ... (remaining 3895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 3878
        1.27 -     2.54: 1007
        2.54 -     3.81: 285
        3.81 -     5.07: 80
        5.07 -     6.34: 40
  Bond angle restraints: 5290
  Sorted by residual:
  angle pdb=" C   VAL A  52 "
        pdb=" CA  VAL A  52 "
        pdb=" CB  VAL A  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.91    5.28 1.39e+00 5.18e-01 1.44e+01
  angle pdb=" C   VAL F  52 "
        pdb=" CA  VAL F  52 "
        pdb=" CB  VAL F  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.93    5.26 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL E  52 "
        pdb=" CA  VAL E  52 "
        pdb=" CB  VAL E  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL H  52 "
        pdb=" CA  VAL H  52 "
        pdb=" CB  VAL H  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL J  52 "
        pdb=" CA  VAL J  52 "
        pdb=" CB  VAL J  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  ... (remaining 5285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.25: 1741
        6.25 -    12.49: 419
       12.49 -    18.73: 60
       18.73 -    24.98: 20
       24.98 -    31.22: 10
  Dihedral angle restraints: 2250
    sinusoidal: 710
      harmonic: 1540
  Sorted by residual:
  dihedral pdb=" CA  GLU F  61 "
           pdb=" C   GLU F  61 "
           pdb=" N   GLN F  62 "
           pdb=" CA  GLN F  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLU G  61 "
           pdb=" C   GLU G  61 "
           pdb=" N   GLN G  62 "
           pdb=" CA  GLN G  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.15   18.85     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLU H  61 "
           pdb=" C   GLU H  61 "
           pdb=" N   GLN H  62 "
           pdb=" CA  GLN H  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.15   18.85     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 2247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 260
       0.045 -    0.089: 241
       0.089 -    0.134: 99
       0.134 -    0.178: 71
       0.178 -    0.222: 39
  Chirality restraints: 710
  Sorted by residual:
  chirality pdb=" CB  VAL H  49 "
            pdb=" CA  VAL H  49 "
            pdb=" CG1 VAL H  49 "
            pdb=" CG2 VAL H  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL C  49 "
            pdb=" CA  VAL C  49 "
            pdb=" CG1 VAL C  49 "
            pdb=" CG2 VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  VAL G  49 "
            pdb=" CA  VAL G  49 "
            pdb=" CG1 VAL G  49 "
            pdb=" CG2 VAL G  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 707 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  81 "   -0.014 2.00e-02 2.50e+03   2.78e-02 7.75e+00
        pdb=" C   THR B  81 "    0.048 2.00e-02 2.50e+03
        pdb=" O   THR B  81 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL B  82 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  81 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.74e+00
        pdb=" C   THR C  81 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR C  81 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL C  82 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  81 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.73e+00
        pdb=" C   THR I  81 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR I  81 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL I  82 "    0.016 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 2504
        3.02 -     3.49: 4006
        3.49 -     3.96: 5893
        3.96 -     4.43: 6914
        4.43 -     4.90: 13870
  Nonbonded interactions: 33187
  Sorted by model distance:
  nonbonded pdb=" N   VAL A  82 "
            pdb=" O   THR C  81 "
     model   vdw
     2.546 3.120
  nonbonded pdb=" N   VAL C  82 "
            pdb=" O   THR E  81 "
     model   vdw
     2.546 3.120
  nonbonded pdb=" N   VAL E  82 "
            pdb=" O   THR G  81 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" N   VAL B  82 "
            pdb=" O   THR D  81 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" N   VAL H  82 "
            pdb=" O   THR J  81 "
     model   vdw
     2.547 3.120
  ... (remaining 33182 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.730
  Find NCS groups from input model:        0.030
  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:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5861
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      :  0.024   0.101   3900  Z= 1.159
  Angle     :  1.403   6.343   5290  Z= 0.831
  Chirality :  0.088   0.222    710
  Planarity :  0.008   0.028    660
  Dihedral  :  7.442  31.218   1290
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.26), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.20), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.027   0.011   TYR C  39 
 HIS   0.009   0.005   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.02423 ( 3900)
  covalent geometry    : angle       1.40288 ( 5290)
  hydrogen bonds       : bond        0.21068 (   56)
  hydrogen bonds       : angle      11.74567 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7607 (tttt) cc_final: 0.7045 (pttm)
REVERT: B   80 LYS cc_start: 0.7372 (tttt) cc_final: 0.6659 (tmmt)
REVERT: C   65 ASN cc_start: 0.6524 (m-40) cc_final: 0.6315 (m-40)
REVERT: E   65 ASN cc_start: 0.6603 (m-40) cc_final: 0.6356 (m-40)
REVERT: F   65 ASN cc_start: 0.6372 (m-40) cc_final: 0.5989 (m-40)
REVERT: G   57 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6108 (mp0)
REVERT: G   65 ASN cc_start: 0.6459 (m-40) cc_final: 0.6230 (m110)
REVERT: I   50 HIS cc_start: 0.6096 (m-70) cc_final: 0.5799 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0544
  time to fit residues: 6.9720
Evaluate side-chains
  82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.240028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.216274 restraints weight = 5620.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.4760 rms_B_bonded: 3.55
r_work: 0.4662 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.4662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4649 r_free = 0.4649    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4628 r_free = 0.4628    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3900  Z= 0.293
  Angle     :  0.796   5.256   5290  Z= 0.458
  Chirality :  0.053   0.174    710
  Planarity :  0.003   0.013    660
  Dihedral  :  6.393  21.657    580
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  6.67 %
    Favored  : 90.51 %
  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 are not related in a simple way.
  whole: -2.02 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR J  39 
 HIS   0.004   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 3900)
  covalent geometry    : angle       0.79560 ( 5290)
  hydrogen bonds       : bond        0.07428 (   56)
  hydrogen bonds       : angle       8.41891 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7569 (tttt) cc_final: 0.6907 (pttp)
REVERT: B   80 LYS cc_start: 0.7572 (tttt) cc_final: 0.6767 (pttm)
REVERT: D   48 VAL cc_start: 0.8210 (t) cc_final: 0.8001 (p)
REVERT: E   80 LYS cc_start: 0.7375 (tttt) cc_final: 0.6882 (tttp)
  outliers start: 11
  outliers final: 9
  residues processed: 121
  average time/residue: 0.0600
  time to fit residues: 9.1209
Evaluate side-chains
  101 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.227939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.205040 restraints weight = 5603.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.4679 rms_B_bonded: 3.46
r_work: 0.4589 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4591 r_free = 0.4591    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4587 r_free = 0.4587    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3900  Z= 0.238
  Angle     :  0.697   5.038   5290  Z= 0.407
  Chirality :  0.051   0.189    710
  Planarity :  0.003   0.013    660
  Dihedral  :  6.078  18.582    580
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 11.03 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR F  39 
 HIS   0.004   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 3900)
  covalent geometry    : angle       0.69655 ( 5290)
  hydrogen bonds       : bond        0.06426 (   56)
  hydrogen bonds       : angle       8.23314 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7505 (tttt) cc_final: 0.6844 (pttp)
REVERT: B   80 LYS cc_start: 0.7503 (tttt) cc_final: 0.6891 (pttp)
REVERT: E   80 LYS cc_start: 0.7377 (tttt) cc_final: 0.6641 (tppt)
  outliers start: 17
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0516
  time to fit residues: 7.5062
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    9.9990
   overall best weight:    3.3184

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.223722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.200928 restraints weight = 5586.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.4647 rms_B_bonded: 3.70
r_work: 0.4552 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3900  Z= 0.226
  Angle     :  0.655   4.907   5290  Z= 0.386
  Chirality :  0.052   0.191    710
  Planarity :  0.003   0.013    660
  Dihedral  :  5.890  16.399    580
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 12.05 %
    Favored  : 81.28 %
  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 are not related in a simple way.
  whole: -2.12 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR F  39 
 HIS   0.004   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 3900)
  covalent geometry    : angle       0.65504 ( 5290)
  hydrogen bonds       : bond        0.06211 (   56)
  hydrogen bonds       : angle       8.10017 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7500 (tttt) cc_final: 0.6907 (pttp)
REVERT: B   80 LYS cc_start: 0.7361 (tttt) cc_final: 0.6883 (pttp)
REVERT: F   80 LYS cc_start: 0.7201 (tttt) cc_final: 0.6456 (tttt)
  outliers start: 26
  outliers final: 21
  residues processed: 116
  average time/residue: 0.0447
  time to fit residues: 6.9547
Evaluate side-chains
  114 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.0870
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.230159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.207177 restraints weight = 5566.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.4713 rms_B_bonded: 3.59
r_work: 0.4629 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3900  Z= 0.129
  Angle     :  0.539   4.657   5290  Z= 0.323
  Chirality :  0.050   0.166    710
  Planarity :  0.002   0.010    660
  Dihedral  :  5.361  15.304    580
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 16.67 %
    Favored  : 77.69 %
  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 are not related in a simple way.
  whole: -2.16 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR G  39 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3900)
  covalent geometry    : angle       0.53918 ( 5290)
  hydrogen bonds       : bond        0.05231 (   56)
  hydrogen bonds       : angle       8.08506 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7468 (tttt) cc_final: 0.7033 (pptt)
REVERT: B   80 LYS cc_start: 0.7322 (tttt) cc_final: 0.6814 (pttp)
REVERT: E   80 LYS cc_start: 0.7240 (tttt) cc_final: 0.6901 (mttm)
  outliers start: 22
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0470
  time to fit residues: 7.7171
Evaluate side-chains
  122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    6.5588

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.208102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.187161 restraints weight = 5887.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.4510 rms_B_bonded: 3.46
r_work: 0.4415 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.6228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   3900  Z= 0.385
  Angle     :  0.818   5.578   5290  Z= 0.471
  Chirality :  0.057   0.216    710
  Planarity :  0.004   0.016    660
  Dihedral  :  6.482  17.425    580
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 21.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.14 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  9.23 %
    Allowed  : 15.64 %
    Favored  : 75.13 %
  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 are not related in a simple way.
  whole: -2.28 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.004   TYR F  39 
 HIS   0.005   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00829 ( 3900)
  covalent geometry    : angle       0.81848 ( 5290)
  hydrogen bonds       : bond        0.06556 (   56)
  hydrogen bonds       : angle       8.40794 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 90
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7671 (tttt) cc_final: 0.7156 (pttp)
REVERT: B   80 LYS cc_start: 0.7480 (tttt) cc_final: 0.7209 (pttp)
REVERT: E   80 LYS cc_start: 0.7500 (tttt) cc_final: 0.6737 (tptt)
REVERT: F   80 LYS cc_start: 0.7435 (tttt) cc_final: 0.6624 (tptt)
REVERT: G   50 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7520 (m-70)
REVERT: H   80 LYS cc_start: 0.7272 (tttt) cc_final: 0.7000 (ttmt)
REVERT: J   80 LYS cc_start: 0.7547 (tttt) cc_final: 0.6957 (tptt)
REVERT: J   88 ILE cc_start: 0.6915 (pt) cc_final: 0.6415 (pt)
  outliers start: 36
  outliers final: 26
  residues processed: 113
  average time/residue: 0.0486
  time to fit residues: 7.2977
Evaluate side-chains
  111 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.223390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.201568 restraints weight = 5539.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4673 rms_B_bonded: 3.36
r_work: 0.4576 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.6260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3900  Z= 0.142
  Angle     :  0.572   5.041   5290  Z= 0.339
  Chirality :  0.051   0.166    710
  Planarity :  0.002   0.011    660
  Dihedral  :  5.626  16.070    580
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 19.23 %
    Favored  : 73.59 %
  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 are not related in a simple way.
  whole: -2.22 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.001   TYR J  39 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3900)
  covalent geometry    : angle       0.57155 ( 5290)
  hydrogen bonds       : bond        0.04988 (   56)
  hydrogen bonds       : angle       8.23572 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7497 (tttt) cc_final: 0.7063 (pttp)
REVERT: F   80 LYS cc_start: 0.6994 (tttt) cc_final: 0.6770 (mttt)
REVERT: H   80 LYS cc_start: 0.7100 (tttt) cc_final: 0.6812 (ttmt)
  outliers start: 28
  outliers final: 24
  residues processed: 120
  average time/residue: 0.0437
  time to fit residues: 7.1556
Evaluate side-chains
  125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.207014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.186021 restraints weight = 5496.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4481 rms_B_bonded: 3.47
r_work: 0.4375 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.6852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3900  Z= 0.365
  Angle     :  0.790   5.637   5290  Z= 0.456
  Chirality :  0.056   0.202    710
  Planarity :  0.004   0.016    660
  Dihedral  :  6.309  17.721    580
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  8.72 %
    Allowed  : 19.23 %
    Favored  : 72.05 %
  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 are not related in a simple way.
  whole: -2.32 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.003   TYR F  39 
 HIS   0.006   0.003   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00799 ( 3900)
  covalent geometry    : angle       0.78955 ( 5290)
  hydrogen bonds       : bond        0.06180 (   56)
  hydrogen bonds       : angle       8.11557 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7619 (tttt) cc_final: 0.7156 (pttp)
REVERT: C   65 ASN cc_start: 0.7247 (m-40) cc_final: 0.7046 (t0)
REVERT: D   80 LYS cc_start: 0.7553 (tttt) cc_final: 0.7023 (mttp)
REVERT: E   80 LYS cc_start: 0.8353 (mttm) cc_final: 0.7230 (tttt)
REVERT: F   80 LYS cc_start: 0.7255 (tttt) cc_final: 0.6446 (tptt)
REVERT: G   80 LYS cc_start: 0.8174 (mttt) cc_final: 0.6956 (tttt)
REVERT: H   80 LYS cc_start: 0.7221 (tttt) cc_final: 0.6994 (ttmt)
REVERT: I   88 ILE cc_start: 0.7092 (pt) cc_final: 0.6635 (pt)
REVERT: J   80 LYS cc_start: 0.7581 (tttt) cc_final: 0.6973 (tptt)
  outliers start: 34
  outliers final: 32
  residues processed: 120
  average time/residue: 0.0484
  time to fit residues: 7.7169
Evaluate side-chains
  126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.218365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.196695 restraints weight = 5440.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.4624 rms_B_bonded: 3.37
r_work: 0.4523 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.6868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3900  Z= 0.167
  Angle     :  0.597   5.968   5290  Z= 0.350
  Chirality :  0.051   0.177    710
  Planarity :  0.002   0.013    660
  Dihedral  :  5.649  16.686    580
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 20.51 %
    Favored  : 72.56 %
  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 are not related in a simple way.
  whole: -2.28 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR J  39 
 HIS   0.003   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3900)
  covalent geometry    : angle       0.59734 ( 5290)
  hydrogen bonds       : bond        0.05104 (   56)
  hydrogen bonds       : angle       8.03069 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7560 (tttt) cc_final: 0.7181 (pttp)
REVERT: E   80 LYS cc_start: 0.8114 (mttm) cc_final: 0.7221 (tttt)
REVERT: G   80 LYS cc_start: 0.8098 (mttt) cc_final: 0.6939 (tttt)
  outliers start: 27
  outliers final: 24
  residues processed: 117
  average time/residue: 0.0485
  time to fit residues: 7.5304
Evaluate side-chains
  125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   overall best weight:    5.0988

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.210069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.189518 restraints weight = 5531.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.4557 rms_B_bonded: 3.27
r_work: 0.4456 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.7225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   3900  Z= 0.298
  Angle     :  0.725   7.019   5290  Z= 0.416
  Chirality :  0.054   0.191    710
  Planarity :  0.003   0.014    660
  Dihedral  :  5.990  17.727    580
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.43 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 21.03 %
    Favored  : 72.05 %
  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 are not related in a simple way.
  whole: -2.34 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR F  39 
 HIS   0.005   0.002   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 ( 3900)
  covalent geometry    : angle       0.72458 ( 5290)
  hydrogen bonds       : bond        0.05751 (   56)
  hydrogen bonds       : angle       7.97232 (  168)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7593 (tttt) cc_final: 0.7222 (pttp)
REVERT: D   80 LYS cc_start: 0.8239 (mttt) cc_final: 0.7180 (tttt)
REVERT: E   60 LYS cc_start: 0.3906 (mtpp) cc_final: 0.3579 (ttmm)
REVERT: G   80 LYS cc_start: 0.8305 (mttt) cc_final: 0.7103 (tttt)
REVERT: H   60 LYS cc_start: 0.4080 (mmmm) cc_final: 0.3569 (tmtt)
REVERT: H   80 LYS cc_start: 0.8039 (mttt) cc_final: 0.7015 (ttmt)
  outliers start: 27
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0535
  time to fit residues: 7.9309
Evaluate side-chains
  121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0000
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.224766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.202662 restraints weight = 5277.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.4695 rms_B_bonded: 3.33
r_work: 0.4591 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6796
moved from start:          0.7276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3900  Z= 0.121
  Angle     :  0.548   5.665   5290  Z= 0.320
  Chirality :  0.051   0.157    710
  Planarity :  0.002   0.010    660
  Dihedral  :  5.282  16.443    580
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 23.08 %
    Favored  : 71.28 %
  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 are not related in a simple way.
  whole: -2.25 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR G  39 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3900)
  covalent geometry    : angle       0.54840 ( 5290)
  hydrogen bonds       : bond        0.04552 (   56)
  hydrogen bonds       : angle       8.08038 (  168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1047.54 seconds
wall clock time: 18 minutes 39.61 seconds (1119.61 seconds total)