Starting phenix.real_space_refine
on Sun Apr  5 02:24:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rb7_53886/04_2026/9rb7_53886.cif"
  }
  resolution = 3.45
  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=   0.001 sd=   0.007
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
     C    2230      2.51       5
     N     630      2.21       5
     O     730      1.98       5
     H    3750      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7340
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 734
          Classifications: {'peptide': 53}
          Link IDs: {'TRANS': 52}
  Restraints were copied for chains:
    A, B, C, D, E, G, H, I, J
  Time building chain proxies: 0.63, per 1000 atoms: 0.09
  Number of scatterers: 7340
  At special positions: 0
  Unit cell: (76.76, 144.632, 42.016, 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)
     O     730      8.00
     N     630      7.00
     C    2230      6.00
     H    3750      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 128.3 milliseconds
  

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 50
      removed outlier: 6.121A  pdb=" N   VAL B  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   VAL F  49 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL H  49 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 66
      removed outlier: 6.459A  pdb=" N   GLN F  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   ASN D  65 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   THR F  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 71
      removed outlier: 6.510A  pdb=" N   VAL B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL F  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL H  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 79
      removed outlier: 6.468A  pdb=" N   ALA B  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ALA B  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ALA F  76 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   GLN H  79 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA F  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA H  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   GLN J  79 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ALA H  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.195A  pdb=" N   VAL A  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   VAL C  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL E  49 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   VAL G  49 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 71
      removed outlier: 6.475A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   VAL E  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL G  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 79
      removed outlier: 6.417A  pdb=" N   ALA A  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   GLN C  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA C  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   GLN E  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ALA E  76 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   GLN G  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ALA E  78 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA G  76 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   GLN I  79 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA G  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54

    35 hydrogen bonds defined for protein.
    105 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        0.82 -     0.98: 3074
        0.98 -     1.14: 676
        1.14 -     1.29: 640
        1.29 -     1.45: 753
        1.45 -     1.60: 2207
  Bond restraints: 7350
  Sorted by residual:
  bond pdb=" ND2 ASN B  65 "
       pdb="HD22 ASN B  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" ND2 ASN G  65 "
       pdb="HD22 ASN G  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" ND2 ASN I  65 "
       pdb="HD22 ASN I  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.65e+01
  bond pdb=" ND2 ASN H  65 "
       pdb="HD22 ASN H  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" ND2 ASN D  65 "
       pdb="HD22 ASN D  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.981 -0.121 2.00e-02 2.50e+03 3.63e+01
  ... (remaining 7345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 11656
        3.15 -     6.31: 1494
        6.31 -     9.46: 150
        9.46 -    12.62: 10
       12.62 -    15.77: 60
  Bond angle restraints: 13370
  Sorted by residual:
  angle pdb=" N   GLY D  51 "
        pdb=" CA  GLY D  51 "
        pdb=" C   GLY D  51 "
      ideal   model   delta    sigma   weight residual
     115.30  130.65  -15.35 1.39e+00 5.18e-01 1.22e+02
  angle pdb=" N   GLY C  51 "
        pdb=" CA  GLY C  51 "
        pdb=" C   GLY C  51 "
      ideal   model   delta    sigma   weight residual
     115.30  130.65  -15.35 1.39e+00 5.18e-01 1.22e+02
  angle pdb=" N   GLY F  51 "
        pdb=" CA  GLY F  51 "
        pdb=" C   GLY F  51 "
      ideal   model   delta    sigma   weight residual
     115.30  130.65  -15.35 1.39e+00 5.18e-01 1.22e+02
  angle pdb=" N   GLY A  51 "
        pdb=" CA  GLY A  51 "
        pdb=" C   GLY A  51 "
      ideal   model   delta    sigma   weight residual
     115.30  130.64  -15.34 1.39e+00 5.18e-01 1.22e+02
  angle pdb=" N   GLY I  51 "
        pdb=" CA  GLY I  51 "
        pdb=" C   GLY I  51 "
      ideal   model   delta    sigma   weight residual
     115.30  130.64  -15.34 1.39e+00 5.18e-01 1.22e+02
  ... (remaining 13365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 3037
       17.20 -    34.39: 199
       34.39 -    51.58: 74
       51.58 -    68.78: 40
       68.78 -    85.97: 20
  Dihedral angle restraints: 3370
    sinusoidal: 1870
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CA  ALA D  89 "
           pdb=" C   ALA D  89 "
           pdb=" N   ALA D  90 "
           pdb=" CA  ALA D  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.21  -16.79     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ALA I  89 "
           pdb=" C   ALA I  89 "
           pdb=" N   ALA I  90 "
           pdb=" CA  ALA I  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.27  -16.73     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  ALA G  89 "
           pdb=" C   ALA G  89 "
           pdb=" N   ALA G  90 "
           pdb=" CA  ALA G  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.062: 300
       0.062 -    0.122: 202
       0.122 -    0.182: 74
       0.182 -    0.242: 54
       0.242 -    0.302: 30
  Chirality restraints: 660
  Sorted by residual:
  chirality pdb=" CA  VAL J  70 "
            pdb=" N   VAL J  70 "
            pdb=" C   VAL J  70 "
            pdb=" CB  VAL J  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  VAL C  70 "
            pdb=" N   VAL C  70 "
            pdb=" C   VAL C  70 "
            pdb=" CB  VAL C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  VAL I  70 "
            pdb=" N   VAL I  70 "
            pdb=" C   VAL I  70 "
            pdb=" CB  VAL I  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 657 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN D  62 "   -0.052 2.00e-02 2.50e+03   4.28e-01 2.75e+03
        pdb=" CD  GLN D  62 "    0.003 2.00e-02 2.50e+03
        pdb=" OE1 GLN D  62 "    0.052 2.00e-02 2.50e+03
        pdb=" NE2 GLN D  62 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN D  62 "    0.739 2.00e-02 2.50e+03
        pdb="HE22 GLN D  62 "   -0.741 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN J  62 "   -0.051 2.00e-02 2.50e+03   4.28e-01 2.75e+03
        pdb=" CD  GLN J  62 "    0.003 2.00e-02 2.50e+03
        pdb=" OE1 GLN J  62 "    0.051 2.00e-02 2.50e+03
        pdb=" NE2 GLN J  62 "    0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN J  62 "    0.739 2.00e-02 2.50e+03
        pdb="HE22 GLN J  62 "   -0.741 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN F  62 "   -0.051 2.00e-02 2.50e+03   4.28e-01 2.75e+03
        pdb=" CD  GLN F  62 "    0.003 2.00e-02 2.50e+03
        pdb=" OE1 GLN F  62 "    0.051 2.00e-02 2.50e+03
        pdb=" NE2 GLN F  62 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN F  62 "    0.738 2.00e-02 2.50e+03
        pdb="HE22 GLN F  62 "   -0.742 2.00e-02 2.50e+03
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.42: 2985
        2.42 -     2.94: 17949
        2.94 -     3.46: 17494
        3.46 -     3.98: 23914
        3.98 -     4.50: 32913
  Nonbonded interactions: 95255
  Sorted by model distance:
  nonbonded pdb="HD21 ASN A  65 "
            pdb=" O   GLY C  68 "
     model   vdw
     1.899 2.450
  nonbonded pdb=" O   GLY F  68 "
            pdb="HD21 ASN D  65 "
     model   vdw
     1.933 2.450
  nonbonded pdb="HD21 ASN F  65 "
            pdb=" O   GLY H  68 "
     model   vdw
     1.942 2.450
  nonbonded pdb="HD21 ASN C  65 "
            pdb=" O   GLY E  68 "
     model   vdw
     1.944 2.450
  nonbonded pdb="HD21 ASN H  65 "
            pdb=" O   GLY J  68 "
     model   vdw
     1.947 2.450
  ... (remaining 95250 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 'F'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.180
  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:             0.040
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
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      :  0.021   0.081   3600  Z= 1.270
  Angle     :  2.894  15.773   4880  Z= 2.044
  Chirality :  0.111   0.302    660
  Planarity :  0.011   0.025    610
  Dihedral  : 13.173  52.597   1190
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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:  0.53 (0.37), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.41 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.004   PHE I  94 
 HIS   0.004   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.02137 ( 3600)
  covalent geometry    : angle       2.89363 ( 4880)
  hydrogen bonds       : bond        0.11059 (   35)
  hydrogen bonds       : angle       5.32916 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7578 (mttt) cc_final: 0.6972 (tptp)
REVERT: F   57 GLU cc_start: 0.8063 (mt-10) cc_final: 0.6795 (tm-30)
REVERT: A   45 LYS cc_start: 0.7689 (mttt) cc_final: 0.7276 (tptp)
REVERT: A   57 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7039 (tm-30)
REVERT: B   45 LYS cc_start: 0.7586 (mttt) cc_final: 0.7362 (tptp)
REVERT: B   57 GLU cc_start: 0.8023 (mt-10) cc_final: 0.6931 (tm-30)
REVERT: C   45 LYS cc_start: 0.7644 (mttt) cc_final: 0.7033 (tptp)
REVERT: D   45 LYS cc_start: 0.7608 (mttt) cc_final: 0.7151 (tptp)
REVERT: D   57 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7763 (mt-10)
REVERT: E   45 LYS cc_start: 0.7490 (mttt) cc_final: 0.7055 (tptp)
REVERT: G   45 LYS cc_start: 0.7550 (mttt) cc_final: 0.7015 (tptp)
REVERT: H   45 LYS cc_start: 0.7629 (mttt) cc_final: 0.6964 (tptp)
REVERT: H   60 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8185 (ttpt)
REVERT: I   45 LYS cc_start: 0.7621 (mttt) cc_final: 0.6950 (tptp)
REVERT: I   57 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7548 (mt-10)
REVERT: I   60 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8315 (tptp)
REVERT: J   45 LYS cc_start: 0.7566 (mttt) cc_final: 0.6959 (tptp)
REVERT: J   57 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7804 (mt-10)
REVERT: J   60 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8300 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2160
  time to fit residues: 32.6985
Evaluate side-chains
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 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 = 0.176606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.157200 restraints weight = 13087.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.4627 rms_B_bonded: 3.23
r_work: 0.4530 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3600  Z= 0.126
  Angle     :  0.570   3.305   4880  Z= 0.364
  Chirality :  0.053   0.142    660
  Planarity :  0.002   0.009    610
  Dihedral  :  8.954  24.741    520
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.22 %
    Favored  : 87.78 %
  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: -0.38 (0.36), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.28 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE A  94 
 HIS   0.001   0.000   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3600)
  covalent geometry    : angle       0.57032 ( 4880)
  hydrogen bonds       : bond        0.01821 (   35)
  hydrogen bonds       : angle       3.51062 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7460 (mttt) cc_final: 0.6896 (tptt)
REVERT: A   45 LYS cc_start: 0.7422 (mttt) cc_final: 0.6791 (tptp)
REVERT: A   46 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6731 (tp30)
REVERT: A   57 GLU cc_start: 0.7903 (mt-10) cc_final: 0.6760 (tm-30)
REVERT: B   45 LYS cc_start: 0.7514 (mttt) cc_final: 0.6868 (tptp)
REVERT: B   46 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6769 (tp30)
REVERT: B   57 GLU cc_start: 0.8033 (mt-10) cc_final: 0.6732 (tm-30)
REVERT: C   45 LYS cc_start: 0.7447 (mttt) cc_final: 0.6833 (tptp)
REVERT: C   60 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7542 (tptp)
REVERT: D   45 LYS cc_start: 0.7490 (mttt) cc_final: 0.6982 (tptp)
REVERT: D   60 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7453 (tptp)
REVERT: E   45 LYS cc_start: 0.7298 (mttt) cc_final: 0.6752 (tptt)
REVERT: G   45 LYS cc_start: 0.7335 (mttt) cc_final: 0.6839 (tptt)
REVERT: G   60 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7362 (tptp)
REVERT: H   45 LYS cc_start: 0.7490 (mttt) cc_final: 0.7043 (tttp)
REVERT: I   45 LYS cc_start: 0.7497 (mttt) cc_final: 0.6987 (tptp)
REVERT: I   57 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7625 (mt-10)
REVERT: I   60 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8432 (ttpt)
REVERT: J   45 LYS cc_start: 0.7691 (mttt) cc_final: 0.7138 (tttp)
REVERT: J   57 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7746 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2562
  time to fit residues: 20.6471
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.165728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.145391 restraints weight = 13857.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4521 rms_B_bonded: 3.14
r_work: 0.4420 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3600  Z= 0.186
  Angle     :  0.560   2.866   4880  Z= 0.355
  Chirality :  0.051   0.141    660
  Planarity :  0.003   0.010    610
  Dihedral  :  8.567  24.923    520
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 12.78 %
    Favored  : 86.67 %
  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: -2.06 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE H  94 
 HIS   0.001   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 3600)
  covalent geometry    : angle       0.55952 ( 4880)
  hydrogen bonds       : bond        0.01763 (   35)
  hydrogen bonds       : angle       3.30881 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7514 (mttt) cc_final: 0.7086 (tttp)
REVERT: F   83 GLU cc_start: 0.8043 (mp0) cc_final: 0.7773 (mp0)
REVERT: A   45 LYS cc_start: 0.7634 (mttt) cc_final: 0.7191 (tptp)
REVERT: A   46 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6968 (tp30)
REVERT: A   57 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7019 (tm-30)
REVERT: B   45 LYS cc_start: 0.7740 (mttt) cc_final: 0.7244 (tptp)
REVERT: C   45 LYS cc_start: 0.7532 (mttt) cc_final: 0.7091 (tttm)
REVERT: C   60 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8089 (ttpt)
REVERT: D   45 LYS cc_start: 0.7648 (mttt) cc_final: 0.7247 (tttm)
REVERT: D   60 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7557 (tptp)
REVERT: E   45 LYS cc_start: 0.7362 (mttt) cc_final: 0.6992 (tttm)
REVERT: G   45 LYS cc_start: 0.7420 (mttt) cc_final: 0.7052 (tttm)
REVERT: G   60 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7433 (tptp)
REVERT: H   45 LYS cc_start: 0.7523 (mttt) cc_final: 0.7163 (tttm)
REVERT: H   83 GLU cc_start: 0.7989 (mp0) cc_final: 0.7594 (mp0)
REVERT: I   45 LYS cc_start: 0.7572 (mttt) cc_final: 0.7124 (tttp)
REVERT: I   60 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8422 (ttpt)
REVERT: J   45 LYS cc_start: 0.7701 (mttt) cc_final: 0.7240 (tttm)
REVERT: J   79 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7810 (mp10)
  outliers start: 2
  outliers final: 1
  residues processed: 72
  average time/residue: 0.2522
  time to fit residues: 20.8332
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain J residue   79 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0170
   chunk 16 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0980
   overall best weight:    1.5220

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.172294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.150569 restraints weight = 13943.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4584 rms_B_bonded: 3.37
r_work: 0.4477 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3600  Z= 0.098
  Angle     :  0.476   2.464   4880  Z= 0.299
  Chirality :  0.052   0.145    660
  Planarity :  0.002   0.013    610
  Dihedral  :  7.806  23.855    520
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.89 %
    Favored  : 84.72 %
  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 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE I  94 
 HIS   0.002   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 3600)
  covalent geometry    : angle       0.47599 ( 4880)
  hydrogen bonds       : bond        0.01083 (   35)
  hydrogen bonds       : angle       3.15202 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7415 (mttt) cc_final: 0.6927 (tttm)
REVERT: F   83 GLU cc_start: 0.7818 (mp0) cc_final: 0.7523 (mp0)
REVERT: A   45 LYS cc_start: 0.7465 (mttt) cc_final: 0.7010 (tptm)
REVERT: A   46 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6882 (tp30)
REVERT: A   57 GLU cc_start: 0.8141 (mt-10) cc_final: 0.6928 (tm-30)
REVERT: B   45 LYS cc_start: 0.7538 (mttt) cc_final: 0.6969 (tttm)
REVERT: B   46 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6797 (tp30)
REVERT: B   57 GLU cc_start: 0.8029 (mt-10) cc_final: 0.6685 (tm-30)
REVERT: B   60 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7626 (tptp)
REVERT: C   45 LYS cc_start: 0.7309 (mttt) cc_final: 0.6805 (tttm)
REVERT: C   60 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7523 (tptp)
REVERT: D   45 LYS cc_start: 0.7450 (mttt) cc_final: 0.6987 (tttm)
REVERT: D   60 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7362 (tptp)
REVERT: E   45 LYS cc_start: 0.7187 (mttt) cc_final: 0.6819 (tttm)
REVERT: G   45 LYS cc_start: 0.7285 (mttt) cc_final: 0.6932 (tttm)
REVERT: G   60 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7235 (tptp)
REVERT: H   45 LYS cc_start: 0.7336 (mttt) cc_final: 0.7091 (tttm)
REVERT: H   83 GLU cc_start: 0.7833 (mp0) cc_final: 0.7301 (mp0)
REVERT: I   45 LYS cc_start: 0.7434 (mttt) cc_final: 0.7107 (tttp)
REVERT: I   60 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8359 (ttpt)
REVERT: J   45 LYS cc_start: 0.7567 (mttt) cc_final: 0.7169 (tttp)
  outliers start: 5
  outliers final: 0
  residues processed: 67
  average time/residue: 0.2524
  time to fit residues: 19.4136
Evaluate side-chains
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.4693 r_free = 0.4693 target = 0.158039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.137319 restraints weight = 14682.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4551 rms_B_bonded: 3.13
r_work: 0.4430 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.4859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3600  Z= 0.281
  Angle     :  0.610   2.839   4880  Z= 0.387
  Chirality :  0.052   0.140    660
  Planarity :  0.004   0.012    610
  Dihedral  :  8.548  24.836    520
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 13.61 %
    Favored  : 86.11 %
  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: -3.72 (0.30), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE I  94 
 HIS   0.002   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 3600)
  covalent geometry    : angle       0.60987 ( 4880)
  hydrogen bonds       : bond        0.02242 (   35)
  hydrogen bonds       : angle       3.83033 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7419 (mttt) cc_final: 0.7102 (tttp)
REVERT: F   60 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7494 (tptp)
REVERT: F   80 LYS cc_start: 0.8090 (tttm) cc_final: 0.7824 (tptp)
REVERT: F   83 GLU cc_start: 0.7957 (mp0) cc_final: 0.7307 (mp0)
REVERT: A   45 LYS cc_start: 0.7689 (mttt) cc_final: 0.7333 (tttm)
REVERT: B   45 LYS cc_start: 0.7793 (mttt) cc_final: 0.7374 (tttm)
REVERT: B   60 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7816 (tptp)
REVERT: C   45 LYS cc_start: 0.7471 (mttt) cc_final: 0.7049 (tttm)
REVERT: C   60 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7718 (tptp)
REVERT: D   45 LYS cc_start: 0.7647 (mttt) cc_final: 0.7274 (tttm)
REVERT: D   60 LYS cc_start: 0.8426 (mtpt) cc_final: 0.7632 (tptp)
REVERT: D   80 LYS cc_start: 0.8148 (tttm) cc_final: 0.7896 (tptp)
REVERT: E   45 LYS cc_start: 0.7397 (mttt) cc_final: 0.7096 (tttp)
REVERT: E   60 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7423 (tptp)
REVERT: E   80 LYS cc_start: 0.8066 (tttm) cc_final: 0.7846 (tptp)
REVERT: E   83 GLU cc_start: 0.7856 (mp0) cc_final: 0.7461 (mp0)
REVERT: G   45 LYS cc_start: 0.7469 (mttt) cc_final: 0.7206 (tttm)
REVERT: G   60 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7358 (tptp)
REVERT: G   80 LYS cc_start: 0.8155 (tttm) cc_final: 0.7926 (tptm)
REVERT: H   80 LYS cc_start: 0.8099 (tttm) cc_final: 0.7823 (tptp)
REVERT: H   83 GLU cc_start: 0.7988 (mp0) cc_final: 0.7742 (mp0)
REVERT: I   45 LYS cc_start: 0.7473 (mttt) cc_final: 0.7249 (tttp)
REVERT: I   60 LYS cc_start: 0.8694 (mtpt) cc_final: 0.7903 (tptp)
REVERT: I   80 LYS cc_start: 0.8329 (tttm) cc_final: 0.7594 (ttpt)
REVERT: J   45 LYS cc_start: 0.7482 (mttt) cc_final: 0.7255 (tttp)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2747
  time to fit residues: 24.1810
Evaluate side-chains
  70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.4763 r_free = 0.4763 target = 0.164336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.143953 restraints weight = 14497.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4620 rms_B_bonded: 3.10
r_work: 0.4507 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.5325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3600  Z= 0.159
  Angle     :  0.519   3.204   4880  Z= 0.328
  Chirality :  0.052   0.138    660
  Planarity :  0.002   0.013    610
  Dihedral  :  8.074  24.535    520
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.11 %
    Favored  : 83.89 %
  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: -3.75 (0.30), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE I  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3600)
  covalent geometry    : angle       0.51909 ( 4880)
  hydrogen bonds       : bond        0.01539 (   35)
  hydrogen bonds       : angle       3.69360 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.192 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.7494 (mttt) cc_final: 0.7148 (tttp)
REVERT: F   60 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7584 (tptp)
REVERT: F   83 GLU cc_start: 0.7941 (mp0) cc_final: 0.7566 (mp0)
REVERT: A   45 LYS cc_start: 0.7811 (mttt) cc_final: 0.7511 (tttp)
REVERT: B   45 LYS cc_start: 0.7836 (mttt) cc_final: 0.7383 (tttm)
REVERT: B   60 LYS cc_start: 0.8570 (mtpt) cc_final: 0.7958 (tptp)
REVERT: C   45 LYS cc_start: 0.7592 (mttt) cc_final: 0.7118 (tttp)
REVERT: C   60 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7786 (tptp)
REVERT: D   45 LYS cc_start: 0.7689 (mttt) cc_final: 0.7302 (tttm)
REVERT: D   60 LYS cc_start: 0.8457 (mtpt) cc_final: 0.7727 (tptp)
REVERT: E   45 LYS cc_start: 0.7458 (mttt) cc_final: 0.7170 (tttp)
REVERT: E   60 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7521 (tptp)
REVERT: G   45 LYS cc_start: 0.7540 (mttt) cc_final: 0.7316 (tttm)
REVERT: G   60 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7530 (tptp)
REVERT: G   83 GLU cc_start: 0.7852 (mp0) cc_final: 0.7567 (mp0)
REVERT: H   83 GLU cc_start: 0.8147 (mp0) cc_final: 0.7924 (mp0)
REVERT: I   60 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8017 (tptp)
REVERT: I   80 LYS cc_start: 0.8316 (tttm) cc_final: 0.7529 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2376
  time to fit residues: 18.9661
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    3.2988

-------------------------------------------------------------------------------
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 = 0.4735 r_free = 0.4735 target = 0.163299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.143001 restraints weight = 14762.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.4575 rms_B_bonded: 3.09
r_work: 0.4454 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.5845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3600  Z= 0.168
  Angle     :  0.528   3.213   4880  Z= 0.332
  Chirality :  0.052   0.138    660
  Planarity :  0.002   0.007    610
  Dihedral  :  7.940  24.222    520
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.84 %
    Favored  : 82.16 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 16.94 %
    Favored  : 82.78 %
  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: -3.80 (0.31), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE I  94 
 HIS   0.004   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3600)
  covalent geometry    : angle       0.52763 ( 4880)
  hydrogen bonds       : bond        0.01652 (   35)
  hydrogen bonds       : angle       3.72698 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7423 (mttt) cc_final: 0.7169 (tttm)
REVERT: F   60 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7589 (tptp)
REVERT: F   83 GLU cc_start: 0.7927 (mp0) cc_final: 0.7518 (mp0)
REVERT: A   45 LYS cc_start: 0.7787 (mttt) cc_final: 0.7553 (tttp)
REVERT: B   45 LYS cc_start: 0.7882 (mttt) cc_final: 0.7454 (tttp)
REVERT: B   60 LYS cc_start: 0.8594 (mtpt) cc_final: 0.7975 (tptp)
REVERT: C   45 LYS cc_start: 0.7631 (mttt) cc_final: 0.7175 (tttp)
REVERT: C   60 LYS cc_start: 0.8505 (mtpt) cc_final: 0.7796 (tptp)
REVERT: C   83 GLU cc_start: 0.8249 (mp0) cc_final: 0.7928 (mp0)
REVERT: D   45 LYS cc_start: 0.7731 (mttt) cc_final: 0.7376 (tttm)
REVERT: D   60 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7728 (tptp)
REVERT: D   83 GLU cc_start: 0.8153 (mp0) cc_final: 0.7936 (mp0)
REVERT: E   45 LYS cc_start: 0.7351 (mttt) cc_final: 0.7133 (tttm)
REVERT: E   60 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7601 (tptp)
REVERT: G   45 LYS cc_start: 0.7559 (mttt) cc_final: 0.7325 (tttm)
REVERT: H   83 GLU cc_start: 0.8147 (mp0) cc_final: 0.7560 (mp0)
REVERT: I   60 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8128 (tptp)
REVERT: I   80 LYS cc_start: 0.8338 (tttm) cc_final: 0.7558 (ttpt)
REVERT: J   80 LYS cc_start: 0.8422 (tttm) cc_final: 0.7555 (ttmt)
  outliers start: 1
  outliers final: 1
  residues processed: 71
  average time/residue: 0.2787
  time to fit residues: 22.3693
Evaluate side-chains
  71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   74 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    2.6586

-------------------------------------------------------------------------------
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 = 0.4681 r_free = 0.4681 target = 0.160738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.140382 restraints weight = 15045.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.4536 rms_B_bonded: 3.22
r_work: 0.4427 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.6000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3600  Z= 0.139
  Angle     :  0.508   3.983   4880  Z= 0.318
  Chirality :  0.052   0.138    660
  Planarity :  0.002   0.010    610
  Dihedral  :  7.755  23.807    520
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.10 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 16.94 %
    Favored  : 82.50 %
  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: -3.65 (0.32), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE I  94 
 HIS   0.003   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3600)
  covalent geometry    : angle       0.50827 ( 4880)
  hydrogen bonds       : bond        0.01299 (   35)
  hydrogen bonds       : angle       3.55352 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.185 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.7382 (mttt) cc_final: 0.7102 (tttm)
REVERT: F   60 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7461 (tptp)
REVERT: F   83 GLU cc_start: 0.7788 (mp0) cc_final: 0.7314 (mp0)
REVERT: A   45 LYS cc_start: 0.7729 (mttt) cc_final: 0.7459 (tttm)
REVERT: B   45 LYS cc_start: 0.7781 (mttt) cc_final: 0.7350 (tttm)
REVERT: B   60 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7839 (tptp)
REVERT: C   45 LYS cc_start: 0.7503 (mttt) cc_final: 0.7049 (tttp)
REVERT: C   60 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7664 (tptp)
REVERT: C   83 GLU cc_start: 0.8108 (mp0) cc_final: 0.7694 (mp0)
REVERT: D   45 LYS cc_start: 0.7561 (mttt) cc_final: 0.7245 (tttm)
REVERT: D   60 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7602 (tptp)
REVERT: E   45 LYS cc_start: 0.7260 (mttt) cc_final: 0.7052 (tttm)
REVERT: E   60 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7445 (tptp)
REVERT: G   45 LYS cc_start: 0.7457 (mttt) cc_final: 0.7139 (tttm)
REVERT: H   83 GLU cc_start: 0.8023 (mp0) cc_final: 0.7730 (mp0)
REVERT: I   60 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8082 (tptp)
REVERT: J   80 LYS cc_start: 0.8356 (tttm) cc_final: 0.7465 (ttpt)
  outliers start: 2
  outliers final: 1
  residues processed: 68
  average time/residue: 0.2651
  time to fit residues: 20.4187
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   74 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.4723 r_free = 0.4723 target = 0.164899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.144523 restraints weight = 14733.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4575 rms_B_bonded: 3.18
r_work: 0.4465 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3600  Z= 0.113
  Angle     :  0.496   6.563   4880  Z= 0.308
  Chirality :  0.052   0.140    660
  Planarity :  0.002   0.010    610
  Dihedral  :  7.421  23.049    520
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.53 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  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: -3.43 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE I  94 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3600)
  covalent geometry    : angle       0.49648 ( 4880)
  hydrogen bonds       : bond        0.01110 (   35)
  hydrogen bonds       : angle       3.40071 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.7336 (mttt) cc_final: 0.7022 (tttm)
REVERT: F   60 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7437 (tptp)
REVERT: F   83 GLU cc_start: 0.7816 (mp0) cc_final: 0.7365 (mp0)
REVERT: A   45 LYS cc_start: 0.7789 (mttt) cc_final: 0.7474 (tttm)
REVERT: A   83 GLU cc_start: 0.8343 (mp0) cc_final: 0.8128 (mp0)
REVERT: B   45 LYS cc_start: 0.7774 (mttt) cc_final: 0.7354 (tttm)
REVERT: C   45 LYS cc_start: 0.7497 (mttt) cc_final: 0.7071 (tttp)
REVERT: C   60 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7698 (tptp)
REVERT: D   45 LYS cc_start: 0.7577 (mttt) cc_final: 0.7073 (tttm)
REVERT: D   60 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7693 (tptp)
REVERT: E   45 LYS cc_start: 0.7300 (mttt) cc_final: 0.7033 (tttm)
REVERT: E   60 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7470 (tptp)
REVERT: G   45 LYS cc_start: 0.7348 (mttt) cc_final: 0.7004 (tttp)
REVERT: H   83 GLU cc_start: 0.8047 (mp0) cc_final: 0.7772 (mp0)
REVERT: I   60 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8169 (tptp)
REVERT: J   80 LYS cc_start: 0.8315 (tttm) cc_final: 0.7452 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2660
  time to fit residues: 19.0744
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 26 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
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 = 0.4653 r_free = 0.4653 target = 0.158808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.138689 restraints weight = 15336.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 3.19
r_work: 0.4395 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.6168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3600  Z= 0.186
  Angle     :  0.545   5.995   4880  Z= 0.340
  Chirality :  0.052   0.140    660
  Planarity :  0.003   0.014    610
  Dihedral  :  7.826  23.748    520
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.25 %
    Favored  : 82.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  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: -3.82 (0.33), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE I  94 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3600)
  covalent geometry    : angle       0.54519 ( 4880)
  hydrogen bonds       : bond        0.01528 (   35)
  hydrogen bonds       : angle       3.62106 (  105)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.186 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.7366 (mttt) cc_final: 0.7066 (tttm)
REVERT: F   60 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7431 (tptp)
REVERT: F   83 GLU cc_start: 0.7831 (mp0) cc_final: 0.7343 (mp0)
REVERT: A   45 LYS cc_start: 0.7923 (mttt) cc_final: 0.7581 (tttm)
REVERT: B   45 LYS cc_start: 0.7849 (mttt) cc_final: 0.7440 (tttm)
REVERT: C   45 LYS cc_start: 0.7527 (mttt) cc_final: 0.7145 (tttm)
REVERT: C   60 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7640 (tptp)
REVERT: D   45 LYS cc_start: 0.7558 (mttt) cc_final: 0.7175 (tttm)
REVERT: D   60 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7650 (tptp)
REVERT: E   45 LYS cc_start: 0.7395 (mttt) cc_final: 0.7126 (tttp)
REVERT: E   60 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7464 (tptp)
REVERT: G   45 LYS cc_start: 0.7396 (mttt) cc_final: 0.7079 (tttm)
REVERT: G   80 LYS cc_start: 0.8094 (tttm) cc_final: 0.7791 (tptp)
REVERT: H   83 GLU cc_start: 0.8001 (mp0) cc_final: 0.7685 (mp0)
REVERT: I   60 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8109 (tptp)
REVERT: I   80 LYS cc_start: 0.8215 (tttm) cc_final: 0.7472 (ttpt)
REVERT: J   80 LYS cc_start: 0.8383 (tttm) cc_final: 0.7493 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2705
  time to fit residues: 21.7747
Evaluate side-chains
  69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.4730 r_free = 0.4730 target = 0.165567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.144748 restraints weight = 14795.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.4587 rms_B_bonded: 3.26
r_work: 0.4473 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.6271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3600  Z= 0.096
  Angle     :  0.491   5.459   4880  Z= 0.302
  Chirality :  0.053   0.139    660
  Planarity :  0.001   0.012    610
  Dihedral  :  7.286  22.685    520
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  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: -3.40 (0.34), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.000   PHE I  94 
 HIS   0.002   0.001   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 3600)
  covalent geometry    : angle       0.49069 ( 4880)
  hydrogen bonds       : bond        0.00939 (   35)
  hydrogen bonds       : angle       3.29736 (  105)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2173.15 seconds
wall clock time: 37 minutes 29.53 seconds (2249.53 seconds total)