Starting phenix.real_space_refine
on Wed Jun  4 23:13:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqw_45825/06_2025/9cqw_45825.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
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: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.05, per 1000 atoms: 0.91
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (77.175, 72.765, 66.885, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 485.9 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      88.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.500A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.699A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.613A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.870A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.143A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 77 through 79
      No H-bonds generated for 'chain 'B' and resid 77 through 79'
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.962A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.709A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.590A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.849A  pdb=" N   GLY D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.569A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 76
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.964A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    341 hydrogen bonds defined for protein.
    975 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: 1.21

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.20 -     1.37: 1498
        1.37 -     1.54: 3041
        1.54 -     1.71: 37
        1.71 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.17e-02 7.31e+03 1.15e+01
  bond pdb=" N   VAL D  23 "
       pdb=" CA  VAL D  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.17e-02 7.31e+03 1.06e+01
  bond pdb=" N   PHE D  42 "
       pdb=" CA  PHE D  42 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.18e-02 7.18e+03 9.54e+00
  bond pdb=" C   PRO A   4 "
       pdb=" O   PRO A   4 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.26e-02 6.30e+03 9.24e+00
  bond pdb=" N   VAL B  67 "
       pdb=" CA  VAL B  67 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.81e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 5691
        1.26 -     2.53: 439
        2.53 -     3.79: 158
        3.79 -     5.06: 30
        5.06 -     6.32: 12
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     111.14  116.45   -5.31 1.08e+00 8.57e-01 2.41e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     111.14  115.86   -4.72 1.08e+00 8.57e-01 1.91e+01
  angle pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
        pdb=" O   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.10    4.07 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" CA  VAL D  23 "
        pdb=" C   VAL D  23 "
        pdb=" O   VAL D  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.28    3.89 1.06e+00 8.90e-01 1.35e+01
  angle pdb=" CA  VAL D  20 "
        pdb=" C   VAL D  20 "
        pdb=" O   VAL D  20 "
      ideal   model   delta    sigma   weight residual
     120.95  117.24    3.71 1.04e+00 9.25e-01 1.27e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2288
       17.87 -    35.74: 224
       35.74 -    53.60: 81
       53.60 -    71.47: 12
       71.47 -    89.34: 9
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CA  ASP C 126 "
           pdb=" CB  ASP C 126 "
           pdb=" CG  ASP C 126 "
           pdb=" OD1 ASP C 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -90.09   60.09     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C1A HEM C 201 "
           pdb=" C2A HEM C 201 "
           pdb=" CAA HEM C 201 "
           pdb=" CBA HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.34  -89.34     2      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C1A HEM A 201 "
           pdb=" C2A HEM A 201 "
           pdb=" CAA HEM A 201 "
           pdb=" CBA HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.43  -87.43     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 565
       0.065 -    0.130: 104
       0.130 -    0.195: 18
       0.195 -    0.259: 3
       0.259 -    0.324: 2
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CB  VAL D 134 "
            pdb=" CA  VAL D 134 "
            pdb=" CG1 VAL D 134 "
            pdb=" CG2 VAL D 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CB  VAL D  18 "
            pdb=" CA  VAL D  18 "
            pdb=" CG1 VAL D  18 "
            pdb=" CG2 VAL D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 123 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO D 124 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 124 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 124 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO B 124 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 124 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO B 125 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 125 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 125 "    0.022 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 83
        2.71 -     3.25: 4305
        3.25 -     3.80: 7714
        3.80 -     4.35: 9849
        4.35 -     4.90: 16056
  Nonbonded interactions: 38007
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 101 "
            pdb=" NH1 ARG D 104 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OE1 GLU B 101 "
            pdb=" NH1 ARG B 104 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   PRO A 114 "
            pdb=" NE2 HIS B 116 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   PRO C 114 "
            pdb=" NE2 HIS D 116 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OE2 GLU C  30 "
            pdb=" ND1 HIS C  50 "
     model   vdw
     2.373 3.120
  ... (remaining 38002 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             19.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.600
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
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      :  0.006   0.124   4614  Z= 0.376
  Angle     :  0.868   6.324   6330  Z= 0.595
  Chirality :  0.057   0.324    692
  Planarity :  0.006   0.048    790
  Dihedral  : 17.308  89.341   1562
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 15.20 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.36), residues: 558
  helix:  2.34 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  0.25 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B  15 
 HIS   0.006   0.001   HIS B  63 
 PHE   0.015   0.002   PHE A  36 
 TYR   0.013   0.002   TYR D 130 
 ARG   0.003   0.001   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12561 (  341)
  hydrogen bonds       : angle       5.21394 (  975)
  covalent geometry    : bond        0.00585 ( 4610)
  covalent geometry    : angle       0.86841 ( 6330)
  Misc. bond           : bond        0.09133 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8077 (tttt) cc_final: 0.7312 (mptm)
REVERT: A  126 ASP cc_start: 0.8067 (t70) cc_final: 0.7792 (t70)
REVERT: B   90 GLU cc_start: 0.7832 (tp30) cc_final: 0.7559 (mm-30)
REVERT: B   99 ASP cc_start: 0.7535 (t70) cc_final: 0.7269 (t70)
REVERT: C   56 LYS cc_start: 0.8043 (tttt) cc_final: 0.7277 (mptm)
REVERT: C   92 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7441 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8070 (t70) cc_final: 0.7780 (t70)
REVERT: C  127 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7890 (mtmt)
REVERT: D   17 LYS cc_start: 0.8390 (mttt) cc_final: 0.7886 (mtpt)
REVERT: D   22 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6546 (mm-30)
REVERT: D   43 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6835 (mm-30)
REVERT: D   65 LYS cc_start: 0.8509 (tttm) cc_final: 0.7953 (ttmt)
REVERT: D   66 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8257 (mtmt)
REVERT: D   90 GLU cc_start: 0.7605 (tt0) cc_final: 0.7164 (mm-30)
REVERT: D  117 HIS cc_start: 0.7600 (t-170) cc_final: 0.6995 (m-70)
REVERT: D  120 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7194 (tptt)
REVERT: D  139 ASN cc_start: 0.7338 (m110) cc_final: 0.7053 (m-40)
  outliers start: 25
  outliers final: 8
  residues processed: 96
  average time/residue: 1.9417
  time to fit residues: 192.0040
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   21 ASP
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 139 ASN
D  19 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.143616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.120331 restraints weight = 4193.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.48
r_work: 0.3260 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.0708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   4614  Z= 0.149
  Angle     :  0.599   5.382   6330  Z= 0.285
  Chirality :  0.041   0.126    692
  Planarity :  0.006   0.049    790
  Dihedral  : 13.055  88.709    637
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 13.88 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.35), residues: 558
  helix:  2.19 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.47 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.013   0.002   PHE D 118 
 TYR   0.010   0.002   TYR D 130 
 ARG   0.003   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  341)
  hydrogen bonds       : angle       4.13644 (  975)
  covalent geometry    : bond        0.00384 ( 4610)
  covalent geometry    : angle       0.59911 ( 6330)
  Misc. bond           : bond        0.06331 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8103 (tttt) cc_final: 0.7377 (mptm)
REVERT: A  126 ASP cc_start: 0.8128 (t70) cc_final: 0.7820 (t70)
REVERT: B   90 GLU cc_start: 0.7959 (tp30) cc_final: 0.7689 (mm-30)
REVERT: B   99 ASP cc_start: 0.7553 (t70) cc_final: 0.7258 (t70)
REVERT: B  132 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8373 (mtmt)
REVERT: C   56 LYS cc_start: 0.8072 (tttt) cc_final: 0.7368 (mptm)
REVERT: C   92 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7532 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8127 (t70) cc_final: 0.7909 (t70)
REVERT: C  127 LYS cc_start: 0.8443 (mtpt) cc_final: 0.7980 (mtmt)
REVERT: D   17 LYS cc_start: 0.8569 (mttt) cc_final: 0.8069 (mtpt)
REVERT: D   22 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6502 (mm-30)
REVERT: D   26 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7535 (mm-30)
REVERT: D   43 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6929 (mm-30)
REVERT: D   65 LYS cc_start: 0.8561 (tttm) cc_final: 0.7994 (ttmt)
REVERT: D   66 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8172 (mtmm)
REVERT: D   82 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8324 (mptt)
REVERT: D   90 GLU cc_start: 0.7689 (tt0) cc_final: 0.7183 (mm-30)
REVERT: D   99 ASP cc_start: 0.7591 (t70) cc_final: 0.7273 (t70)
REVERT: D  117 HIS cc_start: 0.7579 (t-170) cc_final: 0.7008 (m-70)
REVERT: D  120 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7252 (tptp)
  outliers start: 19
  outliers final: 8
  residues processed: 88
  average time/residue: 2.6675
  time to fit residues: 242.3010
Evaluate side-chains
  88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   21 ASP
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.143339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.120352 restraints weight = 4190.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.46
r_work: 0.3250 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.0915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   4614  Z= 0.138
  Angle     :  0.579   5.340   6330  Z= 0.273
  Chirality :  0.040   0.123    692
  Planarity :  0.006   0.048    790
  Dihedral  : 12.708  87.569    634
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 14.32 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.44 (0.63), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.011   0.002   PHE D 118 
 TYR   0.008   0.001   TYR D 130 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  341)
  hydrogen bonds       : angle       3.97341 (  975)
  covalent geometry    : bond        0.00362 ( 4610)
  covalent geometry    : angle       0.57904 ( 6330)
  Misc. bond           : bond        0.05790 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8082 (tttt) cc_final: 0.7356 (mptm)
REVERT: A  126 ASP cc_start: 0.8094 (t70) cc_final: 0.7759 (t70)
REVERT: B   26 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7376 (mm-30)
REVERT: B   99 ASP cc_start: 0.7526 (t70) cc_final: 0.7216 (t70)
REVERT: B  132 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8355 (mtmt)
REVERT: C   56 LYS cc_start: 0.8057 (tttt) cc_final: 0.7351 (mptm)
REVERT: C   92 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7471 (mtt-85)
REVERT: C  126 ASP cc_start: 0.8107 (t70) cc_final: 0.7888 (t70)
REVERT: C  127 LYS cc_start: 0.8475 (mtpt) cc_final: 0.7946 (mtmt)
REVERT: D   17 LYS cc_start: 0.8553 (mttt) cc_final: 0.8010 (mtpt)
REVERT: D   22 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6422 (mm-30)
REVERT: D   26 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7350 (mm-30)
REVERT: D   43 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6989 (mm-30)
REVERT: D   65 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7953 (ttmt)
REVERT: D   66 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8166 (mtmm)
REVERT: D   90 GLU cc_start: 0.7681 (tt0) cc_final: 0.7095 (mm-30)
REVERT: D   95 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7586 (mttm)
REVERT: D   99 ASP cc_start: 0.7554 (t70) cc_final: 0.7213 (t70)
REVERT: D  117 HIS cc_start: 0.7565 (t-170) cc_final: 0.6967 (m-70)
REVERT: D  120 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7121 (tptt)
  outliers start: 22
  outliers final: 5
  residues processed: 86
  average time/residue: 1.7992
  time to fit residues: 159.1104
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0170
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.144240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121238 restraints weight = 4214.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.49
r_work: 0.3269 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4614  Z= 0.118
  Angle     :  0.553   5.282   6330  Z= 0.259
  Chirality :  0.038   0.119    692
  Planarity :  0.006   0.047    790
  Dihedral  : 12.129  87.139    630
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.37 (0.36), residues: 558
  helix:  2.56 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.31 (0.62), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.006   0.001   TYR B 130 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  341)
  hydrogen bonds       : angle       3.85831 (  975)
  covalent geometry    : bond        0.00315 ( 4610)
  covalent geometry    : angle       0.55290 ( 6330)
  Misc. bond           : bond        0.04834 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8045 (tttt) cc_final: 0.7347 (mptm)
REVERT: A  126 ASP cc_start: 0.8071 (t70) cc_final: 0.7794 (t70)
REVERT: B   26 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7306 (mm-30)
REVERT: B   90 GLU cc_start: 0.7922 (tp30) cc_final: 0.7645 (mm-30)
REVERT: B   99 ASP cc_start: 0.7471 (t70) cc_final: 0.7154 (t70)
REVERT: C   56 LYS cc_start: 0.8025 (tttt) cc_final: 0.7354 (mptm)
REVERT: C   92 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7480 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8445 (mtpt) cc_final: 0.7927 (mtmt)
REVERT: D   17 LYS cc_start: 0.8591 (mttt) cc_final: 0.8019 (mtpt)
REVERT: D   22 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6521 (mm-30)
REVERT: D   26 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7306 (mm-30)
REVERT: D   43 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7084 (mm-30)
REVERT: D   65 LYS cc_start: 0.8500 (tttm) cc_final: 0.7929 (ttmt)
REVERT: D   66 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8140 (mtmm)
REVERT: D   90 GLU cc_start: 0.7683 (tt0) cc_final: 0.7082 (mm-30)
REVERT: D   95 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7574 (mttm)
REVERT: D   99 ASP cc_start: 0.7514 (t70) cc_final: 0.7188 (t70)
REVERT: D  117 HIS cc_start: 0.7571 (t-170) cc_final: 0.7016 (m-70)
REVERT: D  120 LYS cc_start: 0.7515 (mmtm) cc_final: 0.7165 (tptt)
  outliers start: 16
  outliers final: 6
  residues processed: 86
  average time/residue: 2.3352
  time to fit residues: 207.1786
Evaluate side-chains
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.5182

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.144538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.121495 restraints weight = 4276.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.51
r_work: 0.3273 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   4614  Z= 0.113
  Angle     :  0.543   5.269   6330  Z= 0.253
  Chirality :  0.038   0.119    692
  Planarity :  0.006   0.046    790
  Dihedral  : 11.989  86.970    630
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.42 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.36), residues: 558
  helix:  2.61 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.22 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.008   0.001   PHE D 118 
 TYR   0.006   0.001   TYR B 130 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  341)
  hydrogen bonds       : angle       3.84742 (  975)
  covalent geometry    : bond        0.00304 ( 4610)
  covalent geometry    : angle       0.54297 ( 6330)
  Misc. bond           : bond        0.04725 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8037 (tttt) cc_final: 0.7379 (mptm)
REVERT: A  126 ASP cc_start: 0.8100 (t70) cc_final: 0.7860 (t70)
REVERT: B   26 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7054 (tm-30)
REVERT: B   90 GLU cc_start: 0.7949 (tp30) cc_final: 0.7678 (mm-30)
REVERT: B   99 ASP cc_start: 0.7465 (t70) cc_final: 0.7157 (t70)
REVERT: C   56 LYS cc_start: 0.8040 (tttt) cc_final: 0.7393 (mptm)
REVERT: C   92 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7503 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8495 (mtpt) cc_final: 0.7987 (mtmt)
REVERT: D   17 LYS cc_start: 0.8650 (mttt) cc_final: 0.8063 (mtpt)
REVERT: D   22 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6627 (mm-30)
REVERT: D   26 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7294 (mm-30)
REVERT: D   43 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7148 (mm-30)
REVERT: D   65 LYS cc_start: 0.8546 (tttm) cc_final: 0.7981 (ttmt)
REVERT: D   66 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8159 (mtmm)
REVERT: D   90 GLU cc_start: 0.7728 (tt0) cc_final: 0.7094 (mm-30)
REVERT: D   95 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7594 (mttm)
REVERT: D   99 ASP cc_start: 0.7523 (t70) cc_final: 0.7196 (t70)
REVERT: D  117 HIS cc_start: 0.7612 (t-170) cc_final: 0.7058 (m-70)
REVERT: D  120 LYS cc_start: 0.7536 (mmtm) cc_final: 0.7255 (tptt)
  outliers start: 17
  outliers final: 7
  residues processed: 85
  average time/residue: 1.7404
  time to fit residues: 152.2102
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.152737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134009 restraints weight = 4238.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.22
r_work: 0.3376 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   4614  Z= 0.122
  Angle     :  0.550   5.299   6330  Z= 0.257
  Chirality :  0.039   0.121    692
  Planarity :  0.006   0.047    790
  Dihedral  : 11.974  86.898    630
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.86 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.32 (0.36), residues: 558
  helix:  2.56 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.18 (0.60), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.006   0.001   TYR B 130 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  341)
  hydrogen bonds       : angle       3.88998 (  975)
  covalent geometry    : bond        0.00324 ( 4610)
  covalent geometry    : angle       0.54998 ( 6330)
  Misc. bond           : bond        0.05217 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7995 (tttt) cc_final: 0.7455 (mptm)
REVERT: A  126 ASP cc_start: 0.8238 (t70) cc_final: 0.7980 (t70)
REVERT: B   26 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7084 (tm-30)
REVERT: B   90 GLU cc_start: 0.7934 (tp30) cc_final: 0.7647 (mm-30)
REVERT: B   99 ASP cc_start: 0.7519 (t70) cc_final: 0.7241 (t70)
REVERT: C   56 LYS cc_start: 0.8047 (tttt) cc_final: 0.7457 (mptm)
REVERT: C   92 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7584 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8058 (mtmt)
REVERT: D   17 LYS cc_start: 0.8717 (mttt) cc_final: 0.8189 (mtpt)
REVERT: D   22 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6711 (mm-30)
REVERT: D   26 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7306 (mm-30)
REVERT: D   43 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7269 (mm-30)
REVERT: D   65 LYS cc_start: 0.8601 (tttm) cc_final: 0.8078 (ttmt)
REVERT: D   66 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8223 (mtmm)
REVERT: D   90 GLU cc_start: 0.7771 (tt0) cc_final: 0.7220 (mm-30)
REVERT: D   95 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7698 (mttm)
REVERT: D   99 ASP cc_start: 0.7563 (t70) cc_final: 0.7258 (t70)
REVERT: D  117 HIS cc_start: 0.7613 (t-170) cc_final: 0.7175 (m-70)
REVERT: D  120 LYS cc_start: 0.7555 (mmtm) cc_final: 0.7310 (tptt)
  outliers start: 16
  outliers final: 8
  residues processed: 86
  average time/residue: 1.6063
  time to fit residues: 142.3543
Evaluate side-chains
  91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.9462

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.149955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.129711 restraints weight = 4232.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.37
r_work: 0.3334 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   4614  Z= 0.153
  Angle     :  0.594   5.462   6330  Z= 0.280
  Chirality :  0.041   0.127    692
  Planarity :  0.006   0.049    790
  Dihedral  : 12.209  86.995    630
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.42 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.35), residues: 558
  helix:  2.31 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.24 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.011   0.002   PHE D 118 
 TYR   0.007   0.001   TYR C 140 
 ARG   0.003   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  341)
  hydrogen bonds       : angle       4.02945 (  975)
  covalent geometry    : bond        0.00399 ( 4610)
  covalent geometry    : angle       0.59421 ( 6330)
  Misc. bond           : bond        0.06666 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8001 (tttt) cc_final: 0.7299 (mptm)
REVERT: A  126 ASP cc_start: 0.8189 (t70) cc_final: 0.7859 (t70)
REVERT: B   26 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7246 (mm-30)
REVERT: B   90 GLU cc_start: 0.7911 (tp30) cc_final: 0.7618 (mm-30)
REVERT: B   99 ASP cc_start: 0.7548 (t70) cc_final: 0.7231 (t70)
REVERT: C   56 LYS cc_start: 0.8025 (tttt) cc_final: 0.7279 (mptm)
REVERT: C   92 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7512 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7955 (mtmt)
REVERT: D   17 LYS cc_start: 0.8680 (mttt) cc_final: 0.8094 (mtpt)
REVERT: D   22 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6637 (mp0)
REVERT: D   26 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7230 (mm-30)
REVERT: D   43 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7246 (mm-30)
REVERT: D   65 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8008 (ttmt)
REVERT: D   66 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8239 (mtmm)
REVERT: D   90 GLU cc_start: 0.7709 (tt0) cc_final: 0.7066 (mm-30)
REVERT: D   95 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7639 (mttm)
REVERT: D   99 ASP cc_start: 0.7582 (t70) cc_final: 0.7239 (t70)
REVERT: D  117 HIS cc_start: 0.7616 (t-170) cc_final: 0.7070 (m-70)
REVERT: D  120 LYS cc_start: 0.7555 (mmtm) cc_final: 0.7176 (tptt)
  outliers start: 18
  outliers final: 8
  residues processed: 85
  average time/residue: 1.4394
  time to fit residues: 126.1930
Evaluate side-chains
  89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0070
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.152385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.133795 restraints weight = 4199.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.20
r_work: 0.3371 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4614  Z= 0.117
  Angle     :  0.546   5.283   6330  Z= 0.255
  Chirality :  0.038   0.119    692
  Planarity :  0.006   0.047    790
  Dihedral  : 11.859  86.761    630
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.86 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.28 (0.36), residues: 558
  helix:  2.49 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.29 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.006   0.001   TYR B 130 
 ARG   0.003   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  341)
  hydrogen bonds       : angle       3.91095 (  975)
  covalent geometry    : bond        0.00314 ( 4610)
  covalent geometry    : angle       0.54570 ( 6330)
  Misc. bond           : bond        0.04889 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8036 (tttt) cc_final: 0.7462 (mptm)
REVERT: A  126 ASP cc_start: 0.8237 (t70) cc_final: 0.7981 (t70)
REVERT: B   26 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7306 (mm-30)
REVERT: B   90 GLU cc_start: 0.7984 (tp30) cc_final: 0.7709 (mm-30)
REVERT: B   95 LYS cc_start: 0.8234 (tttm) cc_final: 0.7550 (mttm)
REVERT: B   99 ASP cc_start: 0.7490 (t70) cc_final: 0.7204 (t70)
REVERT: C   56 LYS cc_start: 0.8063 (tttt) cc_final: 0.7451 (mptm)
REVERT: C   92 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7590 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8070 (mtmt)
REVERT: D   17 LYS cc_start: 0.8700 (mttt) cc_final: 0.8173 (mtpt)
REVERT: D   22 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6711 (mp0)
REVERT: D   26 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7314 (mm-30)
REVERT: D   43 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7311 (mm-30)
REVERT: D   65 LYS cc_start: 0.8609 (tttm) cc_final: 0.8096 (ttmt)
REVERT: D   90 GLU cc_start: 0.7765 (tt0) cc_final: 0.7192 (mm-30)
REVERT: D   95 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7735 (mttm)
REVERT: D   99 ASP cc_start: 0.7521 (t70) cc_final: 0.7210 (t70)
REVERT: D  117 HIS cc_start: 0.7621 (t-170) cc_final: 0.7180 (m-70)
REVERT: D  120 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7372 (tptt)
  outliers start: 15
  outliers final: 7
  residues processed: 83
  average time/residue: 1.4492
  time to fit residues: 124.0448
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.150789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.132079 restraints weight = 4247.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.21
r_work: 0.3342 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   4614  Z= 0.143
  Angle     :  0.582   5.366   6330  Z= 0.274
  Chirality :  0.041   0.126    692
  Planarity :  0.006   0.048    790
  Dihedral  : 12.038  87.305    630
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.08 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.35), residues: 558
  helix:  2.34 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.33 (0.61), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D 116 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.005   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  341)
  hydrogen bonds       : angle       3.98636 (  975)
  covalent geometry    : bond        0.00375 ( 4610)
  covalent geometry    : angle       0.58237 ( 6330)
  Misc. bond           : bond        0.06225 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8080 (tttt) cc_final: 0.7481 (mptm)
REVERT: A  126 ASP cc_start: 0.8236 (t70) cc_final: 0.7901 (t70)
REVERT: B   26 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7335 (mm-30)
REVERT: B   90 GLU cc_start: 0.8005 (tp30) cc_final: 0.7732 (mm-30)
REVERT: B   95 LYS cc_start: 0.8219 (tttm) cc_final: 0.7579 (mttm)
REVERT: B   99 ASP cc_start: 0.7531 (t70) cc_final: 0.7223 (t70)
REVERT: C   56 LYS cc_start: 0.8101 (tttt) cc_final: 0.7473 (mptm)
REVERT: C   92 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7593 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8082 (mtmt)
REVERT: D   17 LYS cc_start: 0.8736 (mttt) cc_final: 0.8195 (mtpt)
REVERT: D   22 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6702 (mp0)
REVERT: D   26 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7308 (mm-30)
REVERT: D   43 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7336 (mm-30)
REVERT: D   65 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8119 (ttmt)
REVERT: D   66 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8270 (mtmm)
REVERT: D   90 GLU cc_start: 0.7791 (tt0) cc_final: 0.7204 (mm-30)
REVERT: D   95 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7735 (mttm)
REVERT: D  117 HIS cc_start: 0.7649 (t-170) cc_final: 0.7194 (m-70)
REVERT: D  120 LYS cc_start: 0.7628 (mmtm) cc_final: 0.7325 (tptt)
  outliers start: 16
  outliers final: 8
  residues processed: 81
  average time/residue: 1.5033
  time to fit residues: 125.3843
Evaluate side-chains
  88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0270
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.152082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.132223 restraints weight = 4185.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.35
r_work: 0.3372 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4614  Z= 0.120
  Angle     :  0.548   5.295   6330  Z= 0.256
  Chirality :  0.039   0.120    692
  Planarity :  0.006   0.047    790
  Dihedral  : 11.781  87.175    630
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.30 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.37 (0.36), residues: 558
  helix:  2.46 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.60 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.005   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  341)
  hydrogen bonds       : angle       3.90423 (  975)
  covalent geometry    : bond        0.00320 ( 4610)
  covalent geometry    : angle       0.54771 ( 6330)
  Misc. bond           : bond        0.04932 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7967 (tttt) cc_final: 0.7300 (mptm)
REVERT: A  126 ASP cc_start: 0.8182 (t70) cc_final: 0.7918 (t70)
REVERT: B   90 GLU cc_start: 0.7957 (tp30) cc_final: 0.7657 (mm-30)
REVERT: B   95 LYS cc_start: 0.8182 (tttm) cc_final: 0.7512 (mttm)
REVERT: B   99 ASP cc_start: 0.7424 (t70) cc_final: 0.7094 (t70)
REVERT: C   56 LYS cc_start: 0.7991 (tttt) cc_final: 0.7286 (mptm)
REVERT: C   92 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7491 (mtt-85)
REVERT: C  127 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7953 (mtmt)
REVERT: D   17 LYS cc_start: 0.8633 (mttt) cc_final: 0.8057 (mtpt)
REVERT: D   22 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6562 (mp0)
REVERT: D   26 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7221 (mm-30)
REVERT: D   43 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7263 (mm-30)
REVERT: D   65 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7978 (ttmt)
REVERT: D   66 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8159 (mtmm)
REVERT: D   90 GLU cc_start: 0.7691 (tt0) cc_final: 0.7062 (mm-30)
REVERT: D   95 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7674 (mttm)
REVERT: D   99 ASP cc_start: 0.7449 (t70) cc_final: 0.7106 (t70)
REVERT: D  117 HIS cc_start: 0.7557 (t-170) cc_final: 0.7044 (m-70)
REVERT: D  120 LYS cc_start: 0.7595 (mmtm) cc_final: 0.7304 (tptt)
  outliers start: 15
  outliers final: 7
  residues processed: 81
  average time/residue: 1.5688
  time to fit residues: 130.9071
Evaluate side-chains
  89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain D residue   22 GLU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.150943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.132356 restraints weight = 4242.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.21
r_work: 0.3345 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   4614  Z= 0.141
  Angle     :  0.579   5.355   6330  Z= 0.273
  Chirality :  0.041   0.125    692
  Planarity :  0.006   0.048    790
  Dihedral  : 11.654  87.560    627
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.52 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.36), residues: 558
  helix:  2.33 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  1.36 (0.62), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D 116 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.010   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  341)
  hydrogen bonds       : angle       3.97698 (  975)
  covalent geometry    : bond        0.00369 ( 4610)
  covalent geometry    : angle       0.57927 ( 6330)
  Misc. bond           : bond        0.05925 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4252.05 seconds
wall clock time: 74 minutes 50.66 seconds (4490.66 seconds total)