Starting phenix.real_space_refine
on Sun May 11 02:28:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvw_43571/05_2025/8vvw_43571.cif"
  }
  resolution = 3.29
  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=  -0.002 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4715      2.51       5
     N    1240      2.21       5
     O    1400      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7380
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1476
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 3, 'TRANS': 180}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.06, per 1000 atoms: 0.69
  Number of scatterers: 7380
  At special positions: 0
  Unit cell: (96.6446, 97.9869, 103.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1400      8.00
     N    1240      7.00
     C    4715      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      76.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 29
    Processing helix  chain 'A' and resid 31 through 37
      removed outlier: 4.300A  pdb=" N   VAL A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 61
    Processing helix  chain 'A' and resid 63 through 66
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 4.636A  pdb=" N   SER A  72 " --> pdb=" O   ASN A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 88
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 112 through 130
    Processing helix  chain 'A' and resid 135 through 146
    Processing helix  chain 'A' and resid 148 through 150
      No H-bonds generated for 'chain 'A' and resid 148 through 150'
    Processing helix  chain 'A' and resid 151 through 161
    Processing helix  chain 'A' and resid 167 through 185
      removed outlier: 3.815A  pdb=" N   LYS A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 29
    Processing helix  chain 'B' and resid 31 through 37
      removed outlier: 4.300A  pdb=" N   VAL B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 61
    Processing helix  chain 'B' and resid 63 through 66
    Processing helix  chain 'B' and resid 67 through 72
      removed outlier: 4.636A  pdb=" N   SER B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 88
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 112 through 130
    Processing helix  chain 'B' and resid 135 through 146
    Processing helix  chain 'B' and resid 148 through 150
      No H-bonds generated for 'chain 'B' and resid 148 through 150'
    Processing helix  chain 'B' and resid 151 through 161
    Processing helix  chain 'B' and resid 167 through 185
      removed outlier: 3.814A  pdb=" N   LYS B 181 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 29
    Processing helix  chain 'C' and resid 31 through 37
      removed outlier: 4.300A  pdb=" N   VAL C  35 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 61
    Processing helix  chain 'C' and resid 63 through 66
    Processing helix  chain 'C' and resid 67 through 72
      removed outlier: 4.636A  pdb=" N   SER C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 88
    Processing helix  chain 'C' and resid 94 through 104
    Processing helix  chain 'C' and resid 112 through 130
    Processing helix  chain 'C' and resid 135 through 146
    Processing helix  chain 'C' and resid 148 through 150
      No H-bonds generated for 'chain 'C' and resid 148 through 150'
    Processing helix  chain 'C' and resid 151 through 161
    Processing helix  chain 'C' and resid 167 through 185
      removed outlier: 3.815A  pdb=" N   LYS C 181 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 29
    Processing helix  chain 'D' and resid 31 through 37
      removed outlier: 4.300A  pdb=" N   VAL D  35 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 61
    Processing helix  chain 'D' and resid 63 through 66
    Processing helix  chain 'D' and resid 67 through 72
      removed outlier: 4.636A  pdb=" N   SER D  72 " --> pdb=" O   ASN D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 88
    Processing helix  chain 'D' and resid 94 through 104
    Processing helix  chain 'D' and resid 112 through 130
    Processing helix  chain 'D' and resid 135 through 146
    Processing helix  chain 'D' and resid 148 through 150
      No H-bonds generated for 'chain 'D' and resid 148 through 150'
    Processing helix  chain 'D' and resid 151 through 161
    Processing helix  chain 'D' and resid 167 through 185
      removed outlier: 3.815A  pdb=" N   LYS D 181 " --> pdb=" O   ASP D 177 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 14 through 29
    Processing helix  chain 'E' and resid 31 through 37
      removed outlier: 4.300A  pdb=" N   VAL E  35 " --> pdb=" O   VAL E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 61
    Processing helix  chain 'E' and resid 63 through 66
    Processing helix  chain 'E' and resid 67 through 72
      removed outlier: 4.637A  pdb=" N   SER E  72 " --> pdb=" O   ASN E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 88
    Processing helix  chain 'E' and resid 94 through 104
    Processing helix  chain 'E' and resid 112 through 130
    Processing helix  chain 'E' and resid 135 through 146
    Processing helix  chain 'E' and resid 148 through 150
      No H-bonds generated for 'chain 'E' and resid 148 through 150'
    Processing helix  chain 'E' and resid 151 through 161
    Processing helix  chain 'E' and resid 167 through 185
      removed outlier: 3.814A  pdb=" N   LYS E 181 " --> pdb=" O   ASP E 177 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1350 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: 1.76

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2410
        1.34 -     1.46: 1492
        1.46 -     1.58: 3543
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7485
  Sorted by residual:
  bond pdb=" C   LEU A 176 "
       pdb=" O   LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.19e-02 7.06e+03 4.86e-01
  bond pdb=" CG1 ILE E 140 "
       pdb=" CD1 ILE E 140 "
    ideal  model  delta    sigma   weight residual
    1.513  1.487  0.026 3.90e-02 6.57e+02 4.41e-01
  bond pdb=" CA  GLU E 179 "
       pdb=" C   GLU E 179 "
    ideal  model  delta    sigma   weight residual
    1.523  1.514  0.009 1.35e-02 5.49e+03 4.33e-01
  bond pdb=" CG1 ILE D 140 "
       pdb=" CD1 ILE D 140 "
    ideal  model  delta    sigma   weight residual
    1.513  1.487  0.026 3.90e-02 6.57e+02 4.28e-01
  bond pdb=" CG1 ILE C 140 "
       pdb=" CD1 ILE C 140 "
    ideal  model  delta    sigma   weight residual
    1.513  1.488  0.025 3.90e-02 6.57e+02 4.22e-01
  ... (remaining 7480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 9916
        1.39 -     2.77: 135
        2.77 -     4.16: 24
        4.16 -     5.54: 0
        5.54 -     6.93: 5
  Bond angle restraints: 10080
  Sorted by residual:
  angle pdb=" CA  LEU B 166 "
        pdb=" CB  LEU B 166 "
        pdb=" CG  LEU B 166 "
      ideal   model   delta    sigma   weight residual
     116.30  123.23   -6.93 3.50e+00 8.16e-02 3.92e+00
  angle pdb=" CA  LEU C 166 "
        pdb=" CB  LEU C 166 "
        pdb=" CG  LEU C 166 "
      ideal   model   delta    sigma   weight residual
     116.30  123.22   -6.92 3.50e+00 8.16e-02 3.91e+00
  angle pdb=" CA  LEU A 166 "
        pdb=" CB  LEU A 166 "
        pdb=" CG  LEU A 166 "
      ideal   model   delta    sigma   weight residual
     116.30  123.21   -6.91 3.50e+00 8.16e-02 3.90e+00
  angle pdb=" CA  LEU E 166 "
        pdb=" CB  LEU E 166 "
        pdb=" CG  LEU E 166 "
      ideal   model   delta    sigma   weight residual
     116.30  123.20   -6.90 3.50e+00 8.16e-02 3.88e+00
  angle pdb=" CA  LEU D 166 "
        pdb=" CB  LEU D 166 "
        pdb=" CG  LEU D 166 "
      ideal   model   delta    sigma   weight residual
     116.30  123.18   -6.88 3.50e+00 8.16e-02 3.86e+00
  ... (remaining 10075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 4138
       15.57 -    31.13: 377
       31.13 -    46.70: 110
       46.70 -    62.27: 15
       62.27 -    77.84: 5
  Dihedral angle restraints: 4645
    sinusoidal: 1910
      harmonic: 2735
  Sorted by residual:
  dihedral pdb=" CG  ARG D 174 "
           pdb=" CD  ARG D 174 "
           pdb=" NE  ARG D 174 "
           pdb=" CZ  ARG D 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.98  -41.98     2      1.50e+01 4.44e-03 9.55e+00
  dihedral pdb=" CG  ARG E 174 "
           pdb=" CD  ARG E 174 "
           pdb=" NE  ARG E 174 "
           pdb=" CZ  ARG E 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.94  -41.94     2      1.50e+01 4.44e-03 9.53e+00
  dihedral pdb=" CG  ARG A 174 "
           pdb=" CD  ARG A 174 "
           pdb=" NE  ARG A 174 "
           pdb=" CZ  ARG A 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.93  -41.93     2      1.50e+01 4.44e-03 9.53e+00
  ... (remaining 4642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 775
       0.028 -    0.056: 313
       0.056 -    0.084: 76
       0.084 -    0.112: 13
       0.112 -    0.140: 13
  Chirality restraints: 1190
  Sorted by residual:
  chirality pdb=" CA  GLN E 178 "
            pdb=" N   GLN E 178 "
            pdb=" C   GLN E 178 "
            pdb=" CB  GLN E 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  GLN D 178 "
            pdb=" N   GLN D 178 "
            pdb=" C   GLN D 178 "
            pdb=" CB  GLN D 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  GLN C 178 "
            pdb=" N   GLN C 178 "
            pdb=" C   GLN C 178 "
            pdb=" CB  GLN C 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 1187 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  31 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.16e+00
        pdb=" C   VAL B  31 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   VAL B  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU B  32 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  31 "    0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   VAL C  31 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   VAL C  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU C  32 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  31 "    0.005 2.00e-02 2.50e+03   1.07e-02 1.14e+00
        pdb=" C   VAL D  31 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL D  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU D  32 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2070
        2.82 -     3.34: 7114
        3.34 -     3.86: 11922
        3.86 -     4.38: 12987
        4.38 -     4.90: 23532
  Nonbonded interactions: 57625
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  15 "
            pdb=" OD1 ASP D  84 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OH  TYR A  15 "
            pdb=" OD1 ASP A  84 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR C  15 "
            pdb=" OD1 ASP C  84 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR B  15 "
            pdb=" OD1 ASP B  84 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR E  15 "
            pdb=" OD1 ASP E  84 "
     model   vdw
     2.297 3.040
  ... (remaining 57620 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  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:             34.180
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.180
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
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      :  0.003   0.026   7485  Z= 0.111
  Angle     :  0.423   6.926  10080  Z= 0.230
  Chirality :  0.034   0.140   1190
  Planarity :  0.002   0.014   1260
  Dihedral  : 13.091  77.836   2845
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.54 (0.29), residues: 910
  helix:  2.11 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.91 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  18 
 HIS   0.001   0.000   HIS A 116 
 PHE   0.002   0.001   PHE D  10 
 TYR   0.013   0.002   TYR A  61 
 ARG   0.001   0.000   ARG C 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09737 (  455)
  hydrogen bonds       : angle       4.48784 ( 1350)
  covalent geometry    : bond        0.00252 ( 7485)
  covalent geometry    : angle       0.42315 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.9016 (mttt) cc_final: 0.8788 (mttm)
REVERT: A   48 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7770 (mttp)
REVERT: A   51 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7720 (mm-30)
REVERT: A  100 LYS cc_start: 0.8656 (mtmt) cc_final: 0.7694 (mmtt)
REVERT: A  180 ILE cc_start: 0.8612 (mm) cc_final: 0.8409 (mt)
REVERT: B   39 MET cc_start: 0.7761 (tpt) cc_final: 0.7483 (mmp)
REVERT: B   48 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8027 (mtmm)
REVERT: B   49 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7550 (ttpp)
REVERT: B   77 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7793 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7537 (ttpp)
REVERT: B  111 MET cc_start: 0.7941 (ttm) cc_final: 0.7601 (ttp)
REVERT: C   14 LYS cc_start: 0.9048 (mttt) cc_final: 0.8777 (mttt)
REVERT: C   51 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7833 (mm-30)
REVERT: C   74 ILE cc_start: 0.8737 (pt) cc_final: 0.8519 (pt)
REVERT: C  100 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7305 (mmtt)
REVERT: C  136 GLU cc_start: 0.8689 (tp30) cc_final: 0.8486 (mm-30)
REVERT: C  137 MET cc_start: 0.8179 (tpp) cc_final: 0.7846 (tpp)
REVERT: C  155 ILE cc_start: 0.8965 (mm) cc_final: 0.8758 (mm)
REVERT: C  159 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: C  177 ASP cc_start: 0.7849 (t0) cc_final: 0.7635 (t0)
REVERT: D   49 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6891 (mmmt)
REVERT: D   51 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: D   59 ILE cc_start: 0.9141 (mt) cc_final: 0.8901 (mt)
REVERT: D  100 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8088 (tttt)
REVERT: D  111 MET cc_start: 0.8449 (ttm) cc_final: 0.8117 (ttp)
REVERT: D  121 ASP cc_start: 0.8167 (m-30) cc_final: 0.7944 (m-30)
REVERT: D  159 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7565 (mt-10)
REVERT: E    6 ASN cc_start: 0.8397 (t0) cc_final: 0.8161 (t0)
REVERT: E   28 GLU cc_start: 0.8096 (tt0) cc_final: 0.7768 (tt0)
REVERT: E   61 TYR cc_start: 0.8969 (m-80) cc_final: 0.8709 (m-80)
REVERT: E   84 ASP cc_start: 0.8538 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2365
  time to fit residues: 73.5823
Evaluate side-chains
  171 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
C   6 ASN
D   6 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.121484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.096898 restraints weight = 8978.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.92
r_work: 0.2814 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2643 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7485  Z= 0.142
  Angle     :  0.485   7.410  10080  Z= 0.261
  Chirality :  0.036   0.137   1190
  Planarity :  0.003   0.019   1260
  Dihedral  :  3.315  15.424    980
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.41 %
    Favored  : 90.73 %
  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:  2.80 (0.28), residues: 910
  helix:  2.33 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.98 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  18 
 HIS   0.002   0.000   HIS A 116 
 PHE   0.006   0.001   PHE D  10 
 TYR   0.016   0.002   TYR D  61 
 ARG   0.004   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  455)
  hydrogen bonds       : angle       3.96395 ( 1350)
  covalent geometry    : bond        0.00328 ( 7485)
  covalent geometry    : angle       0.48485 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 209
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7570 (mtmm)
REVERT: A   60 GLU cc_start: 0.8832 (tt0) cc_final: 0.8565 (tt0)
REVERT: A  165 ASN cc_start: 0.8952 (t0) cc_final: 0.8674 (t0)
REVERT: B   39 MET cc_start: 0.7835 (tpt) cc_final: 0.7427 (mmp)
REVERT: B   48 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7940 (mtmm)
REVERT: B   60 GLU cc_start: 0.8516 (tt0) cc_final: 0.8247 (tt0)
REVERT: B   77 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7680 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7049 (ttpp)
REVERT: B  111 MET cc_start: 0.8109 (ttm) cc_final: 0.7555 (ttp)
REVERT: C   42 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: C   51 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: C  100 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7517 (ttmm)
REVERT: C  122 GLU cc_start: 0.8701 (tt0) cc_final: 0.8281 (mt-10)
REVERT: C  159 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8111 (mt-10)
REVERT: C  166 LEU cc_start: 0.8680 (pt) cc_final: 0.8412 (pt)
REVERT: C  177 ASP cc_start: 0.8080 (t0) cc_final: 0.7757 (t0)
REVERT: C  180 ILE cc_start: 0.8519 (mt) cc_final: 0.8303 (mt)
REVERT: D   49 LYS cc_start: 0.6788 (tmtt) cc_final: 0.6399 (ttpp)
REVERT: D   77 ARG cc_start: 0.8299 (ttt180) cc_final: 0.8025 (ttt90)
REVERT: D  100 LYS cc_start: 0.8560 (mtmt) cc_final: 0.7654 (tttp)
REVERT: D  159 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: D  179 GLU cc_start: 0.8489 (tt0) cc_final: 0.8271 (tt0)
REVERT: E    6 ASN cc_start: 0.8608 (t0) cc_final: 0.8327 (t0)
REVERT: E   84 ASP cc_start: 0.8722 (m-30) cc_final: 0.8256 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 214
  average time/residue: 0.2077
  time to fit residues: 57.9473
Evaluate side-chains
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 182
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain C residue   64 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.125008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.100236 restraints weight = 9058.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.99
r_work: 0.2861 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7485  Z= 0.133
  Angle     :  0.471   7.760  10080  Z= 0.254
  Chirality :  0.036   0.143   1190
  Planarity :  0.003   0.024   1260
  Dihedral  :  3.336  14.969    980
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.00 %
    Favored  : 87.93 %
  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:  2.88 (0.28), residues: 910
  helix:  2.40 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.96 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.002   0.000   HIS E 118 
 PHE   0.004   0.001   PHE D  10 
 TYR   0.018   0.002   TYR E  61 
 ARG   0.003   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  455)
  hydrogen bonds       : angle       3.89159 ( 1350)
  covalent geometry    : bond        0.00304 ( 7485)
  covalent geometry    : angle       0.47053 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8329 (t0) cc_final: 0.8122 (t0)
REVERT: A   48 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7814 (mtmm)
REVERT: A  164 GLU cc_start: 0.8499 (mp0) cc_final: 0.8159 (mp0)
REVERT: A  165 ASN cc_start: 0.8932 (t0) cc_final: 0.8526 (t0)
REVERT: B   39 MET cc_start: 0.7798 (tpt) cc_final: 0.7428 (mmp)
REVERT: B   77 ARG cc_start: 0.8345 (ttt180) cc_final: 0.8026 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7375 (ttpp)
REVERT: B  111 MET cc_start: 0.8285 (ttm) cc_final: 0.7763 (ttp)
REVERT: C  100 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7688 (ttmm)
REVERT: C  122 GLU cc_start: 0.8760 (tt0) cc_final: 0.8459 (mt-10)
REVERT: C  159 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8206 (mt-10)
REVERT: C  165 ASN cc_start: 0.8973 (t0) cc_final: 0.8772 (t0)
REVERT: C  166 LEU cc_start: 0.8834 (pt) cc_final: 0.8557 (pt)
REVERT: C  177 ASP cc_start: 0.8183 (t0) cc_final: 0.7878 (t0)
REVERT: C  180 ILE cc_start: 0.8642 (mt) cc_final: 0.8431 (mt)
REVERT: D   49 LYS cc_start: 0.6954 (tmtt) cc_final: 0.6681 (mmmt)
REVERT: D  100 LYS cc_start: 0.8681 (mtmt) cc_final: 0.7947 (tttp)
REVERT: D  159 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: D  179 GLU cc_start: 0.8556 (tt0) cc_final: 0.8260 (tt0)
REVERT: E    6 ASN cc_start: 0.8637 (t0) cc_final: 0.8321 (t0)
REVERT: E   84 ASP cc_start: 0.8856 (m-30) cc_final: 0.8473 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 205
  average time/residue: 0.2228
  time to fit residues: 58.6266
Evaluate side-chains
  185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain D residue    6 ASN
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.120595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.096105 restraints weight = 9078.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.95
r_work: 0.2867 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7485  Z= 0.136
  Angle     :  0.471   7.898  10080  Z= 0.254
  Chirality :  0.036   0.141   1190
  Planarity :  0.003   0.026   1260
  Dihedral  :  3.336  15.032    980
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.98 %
    Favored  : 86.95 %
  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:  2.86 (0.28), residues: 910
  helix:  2.40 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.95 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.002   0.000   HIS E 118 
 PHE   0.004   0.001   PHE B  10 
 TYR   0.014   0.002   TYR A  61 
 ARG   0.002   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  455)
  hydrogen bonds       : angle       3.85712 ( 1350)
  covalent geometry    : bond        0.00316 ( 7485)
  covalent geometry    : angle       0.47071 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8522 (t0) cc_final: 0.8312 (t0)
REVERT: A   48 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7706 (mtmm)
REVERT: A  164 GLU cc_start: 0.8523 (mp0) cc_final: 0.8184 (mp0)
REVERT: A  165 ASN cc_start: 0.8932 (t0) cc_final: 0.8602 (t0)
REVERT: B   39 MET cc_start: 0.7794 (tpt) cc_final: 0.7475 (mmm)
REVERT: B   77 ARG cc_start: 0.8349 (ttt180) cc_final: 0.7921 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7228 (ttpp)
REVERT: B  111 MET cc_start: 0.8151 (ttm) cc_final: 0.7748 (ttp)
REVERT: C   42 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7773 (tm-30)
REVERT: C  100 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7585 (ttmm)
REVERT: C  122 GLU cc_start: 0.8726 (tt0) cc_final: 0.8387 (mt-10)
REVERT: C  159 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8237 (mt-10)
REVERT: C  165 ASN cc_start: 0.8982 (t0) cc_final: 0.8706 (t0)
REVERT: C  177 ASP cc_start: 0.8124 (t0) cc_final: 0.7809 (t0)
REVERT: C  180 ILE cc_start: 0.8590 (mt) cc_final: 0.8388 (mt)
REVERT: C  182 ILE cc_start: 0.8137 (mt) cc_final: 0.7904 (mp)
REVERT: D   49 LYS cc_start: 0.6912 (tmtt) cc_final: 0.6661 (mmmt)
REVERT: D   60 GLU cc_start: 0.8431 (tt0) cc_final: 0.8065 (tt0)
REVERT: D   87 TYR cc_start: 0.9021 (m-80) cc_final: 0.8799 (m-80)
REVERT: D  100 LYS cc_start: 0.8674 (mtmt) cc_final: 0.7812 (tttp)
REVERT: D  101 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8421 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: E    6 ASN cc_start: 0.8585 (t0) cc_final: 0.8175 (t0)
REVERT: E   84 ASP cc_start: 0.8815 (m-30) cc_final: 0.8417 (m-30)
  outliers start: 17
  outliers final: 7
  residues processed: 213
  average time/residue: 0.2334
  time to fit residues: 64.5965
Evaluate side-chains
  194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    0.4980
   chunk 79 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.120025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.096257 restraints weight = 9067.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.89
r_work: 0.2853 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7485  Z= 0.136
  Angle     :  0.473   8.029  10080  Z= 0.256
  Chirality :  0.036   0.147   1190
  Planarity :  0.003   0.029   1260
  Dihedral  :  3.338  14.184    980
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.46 %
    Favored  : 86.34 %
  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:  2.85 (0.28), residues: 910
  helix:  2.40 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.91 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.002   0.000   HIS E 118 
 PHE   0.004   0.001   PHE B 120 
 TYR   0.017   0.002   TYR C  61 
 ARG   0.002   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  455)
  hydrogen bonds       : angle       3.88092 ( 1350)
  covalent geometry    : bond        0.00314 ( 7485)
  covalent geometry    : angle       0.47259 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7755 (mtmm)
REVERT: A   60 GLU cc_start: 0.8665 (tt0) cc_final: 0.8333 (tt0)
REVERT: A  100 LYS cc_start: 0.8744 (mtmt) cc_final: 0.7820 (ttpt)
REVERT: A  164 GLU cc_start: 0.8493 (mp0) cc_final: 0.8174 (mp0)
REVERT: A  165 ASN cc_start: 0.8920 (t0) cc_final: 0.8588 (t0)
REVERT: B   39 MET cc_start: 0.7907 (tpt) cc_final: 0.7478 (mmm)
REVERT: B   77 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7853 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7209 (ttpp)
REVERT: B  111 MET cc_start: 0.8182 (ttm) cc_final: 0.7773 (ttp)
REVERT: C  100 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7630 (ttmm)
REVERT: C  122 GLU cc_start: 0.8605 (tt0) cc_final: 0.8343 (mt-10)
REVERT: C  159 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: C  165 ASN cc_start: 0.8954 (t0) cc_final: 0.8627 (t0)
REVERT: C  177 ASP cc_start: 0.8094 (t0) cc_final: 0.7772 (t0)
REVERT: D   49 LYS cc_start: 0.6933 (tmtt) cc_final: 0.6670 (mmmt)
REVERT: D   60 GLU cc_start: 0.8439 (tt0) cc_final: 0.8067 (tt0)
REVERT: D   87 TYR cc_start: 0.8998 (m-80) cc_final: 0.8795 (m-80)
REVERT: D  100 LYS cc_start: 0.8682 (mtmt) cc_final: 0.7819 (tttp)
REVERT: D  101 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8419 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: E    6 ASN cc_start: 0.8506 (t0) cc_final: 0.8100 (t0)
REVERT: E   84 ASP cc_start: 0.8810 (m-30) cc_final: 0.8401 (m-30)
REVERT: E  159 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8055 (mp0)
  outliers start: 18
  outliers final: 15
  residues processed: 203
  average time/residue: 0.2365
  time to fit residues: 62.0467
Evaluate side-chains
  193 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain D residue    6 ASN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0770
   chunk 38 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.122137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097321 restraints weight = 9086.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.00
r_work: 0.2870 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7485  Z= 0.112
  Angle     :  0.449   8.057  10080  Z= 0.245
  Chirality :  0.035   0.147   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.284  13.377    980
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.68 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.91 (0.28), residues: 910
  helix:  2.46 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.89 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 118 
 PHE   0.005   0.001   PHE B 120 
 TYR   0.017   0.002   TYR E  61 
 ARG   0.002   0.000   ARG D 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  455)
  hydrogen bonds       : angle       3.83578 ( 1350)
  covalent geometry    : bond        0.00247 ( 7485)
  covalent geometry    : angle       0.44940 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7840 (mtmm)
REVERT: A   60 GLU cc_start: 0.8685 (tt0) cc_final: 0.8397 (tt0)
REVERT: A  100 LYS cc_start: 0.8775 (mtmt) cc_final: 0.7907 (ttpt)
REVERT: A  164 GLU cc_start: 0.8499 (mp0) cc_final: 0.8219 (mp0)
REVERT: A  165 ASN cc_start: 0.8917 (t0) cc_final: 0.8587 (t0)
REVERT: B   39 MET cc_start: 0.7922 (tpt) cc_final: 0.7514 (mmm)
REVERT: B   44 ASP cc_start: 0.7445 (t70) cc_final: 0.7042 (p0)
REVERT: B   45 ASP cc_start: 0.7747 (t0) cc_final: 0.7473 (t0)
REVERT: B   77 ARG cc_start: 0.8373 (ttt180) cc_final: 0.8048 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7325 (ttpp)
REVERT: B  111 MET cc_start: 0.8181 (ttm) cc_final: 0.7789 (ttp)
REVERT: C  100 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7723 (ttmm)
REVERT: C  122 GLU cc_start: 0.8679 (tt0) cc_final: 0.8453 (mt-10)
REVERT: C  159 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: C  165 ASN cc_start: 0.9032 (t0) cc_final: 0.8649 (t0)
REVERT: C  177 ASP cc_start: 0.8148 (t0) cc_final: 0.7909 (t0)
REVERT: D   49 LYS cc_start: 0.7023 (tmtt) cc_final: 0.6786 (mmmt)
REVERT: D   60 GLU cc_start: 0.8420 (tt0) cc_final: 0.8076 (tt0)
REVERT: D   87 TYR cc_start: 0.8978 (m-80) cc_final: 0.8448 (m-80)
REVERT: D  100 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8011 (tttp)
REVERT: D  101 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8461 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: E    6 ASN cc_start: 0.8522 (t0) cc_final: 0.8115 (t0)
REVERT: E   39 MET cc_start: 0.7785 (tpp) cc_final: 0.7564 (tpp)
REVERT: E   84 ASP cc_start: 0.8795 (m-30) cc_final: 0.8403 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2272
  time to fit residues: 59.6086
Evaluate side-chains
  191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0870
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
D   6 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.121267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.096286 restraints weight = 9044.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.00
r_work: 0.2773 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7485  Z= 0.138
  Angle     :  0.478   8.131  10080  Z= 0.259
  Chirality :  0.037   0.158   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.304  13.426    980
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.54 %
    Favored  : 84.27 %
  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:  2.80 (0.28), residues: 910
  helix:  2.39 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.82 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.001   0.000   HIS E 118 
 PHE   0.005   0.001   PHE B  10 
 TYR   0.019   0.002   TYR E  61 
 ARG   0.003   0.000   ARG B   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  455)
  hydrogen bonds       : angle       3.87482 ( 1350)
  covalent geometry    : bond        0.00319 ( 7485)
  covalent geometry    : angle       0.47796 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8443 (t0) cc_final: 0.8180 (t0)
REVERT: A   48 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7820 (mtmm)
REVERT: A   60 GLU cc_start: 0.8727 (tt0) cc_final: 0.8439 (tt0)
REVERT: A  100 LYS cc_start: 0.8773 (mtmt) cc_final: 0.7863 (ttpt)
REVERT: A  164 GLU cc_start: 0.8551 (mp0) cc_final: 0.8259 (mp0)
REVERT: A  165 ASN cc_start: 0.8920 (t0) cc_final: 0.8567 (t0)
REVERT: B   39 MET cc_start: 0.7969 (tpt) cc_final: 0.7525 (mmm)
REVERT: B   44 ASP cc_start: 0.7402 (t70) cc_final: 0.6992 (p0)
REVERT: B   77 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8073 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7350 (ttpp)
REVERT: B  111 MET cc_start: 0.8218 (ttm) cc_final: 0.7818 (ttp)
REVERT: C  100 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7755 (ttmm)
REVERT: C  122 GLU cc_start: 0.8744 (tt0) cc_final: 0.8421 (mt-10)
REVERT: C  159 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8349 (mt-10)
REVERT: C  165 ASN cc_start: 0.9038 (t0) cc_final: 0.8668 (t0)
REVERT: C  177 ASP cc_start: 0.8159 (t0) cc_final: 0.7923 (t0)
REVERT: D   49 LYS cc_start: 0.7062 (tmtt) cc_final: 0.6809 (mmmt)
REVERT: D   60 GLU cc_start: 0.8476 (tt0) cc_final: 0.8121 (tt0)
REVERT: D   87 TYR cc_start: 0.9031 (m-80) cc_final: 0.8756 (m-80)
REVERT: D  100 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8012 (tttp)
REVERT: D  101 ARG cc_start: 0.8726 (ttm170) cc_final: 0.8485 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7804 (mt-10)
REVERT: E    6 ASN cc_start: 0.8551 (t0) cc_final: 0.8100 (t0)
REVERT: E   39 MET cc_start: 0.7829 (tpp) cc_final: 0.7592 (tpp)
REVERT: E   84 ASP cc_start: 0.8814 (m-30) cc_final: 0.8437 (m-30)
REVERT: E  159 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8138 (mp0)
  outliers start: 18
  outliers final: 16
  residues processed: 197
  average time/residue: 0.2453
  time to fit residues: 61.5317
Evaluate side-chains
  210 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain D residue    6 ASN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN
E 184 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.121486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.096857 restraints weight = 9051.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.96
r_work: 0.2806 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7485  Z= 0.135
  Angle     :  0.483   8.129  10080  Z= 0.262
  Chirality :  0.036   0.161   1190
  Planarity :  0.003   0.032   1260
  Dihedral  :  3.296  13.294    980
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.15 %
    Favored  : 83.29 %
  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:  2.80 (0.28), residues: 910
  helix:  2.39 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.83 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.001   0.000   HIS E 118 
 PHE   0.005   0.001   PHE B 120 
 TYR   0.019   0.002   TYR E  61 
 ARG   0.003   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  455)
  hydrogen bonds       : angle       3.86205 ( 1350)
  covalent geometry    : bond        0.00311 ( 7485)
  covalent geometry    : angle       0.48292 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8515 (t0) cc_final: 0.8279 (t0)
REVERT: A   48 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7807 (mtmm)
REVERT: A   60 GLU cc_start: 0.8853 (tt0) cc_final: 0.8601 (tt0)
REVERT: A  100 LYS cc_start: 0.8754 (mtmt) cc_final: 0.7839 (ttpt)
REVERT: A  164 GLU cc_start: 0.8550 (mp0) cc_final: 0.8288 (mp0)
REVERT: A  165 ASN cc_start: 0.8931 (t0) cc_final: 0.8590 (t0)
REVERT: B   39 MET cc_start: 0.7946 (tpt) cc_final: 0.7512 (mmm)
REVERT: B   44 ASP cc_start: 0.7380 (t70) cc_final: 0.6971 (p0)
REVERT: B   77 ARG cc_start: 0.8406 (ttt180) cc_final: 0.7898 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7315 (ttpp)
REVERT: B  111 MET cc_start: 0.8216 (ttm) cc_final: 0.7815 (ttp)
REVERT: C  100 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7725 (ttmm)
REVERT: C  122 GLU cc_start: 0.8705 (tt0) cc_final: 0.8385 (mt-10)
REVERT: C  159 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8336 (mt-10)
REVERT: C  165 ASN cc_start: 0.9030 (t0) cc_final: 0.8693 (t0)
REVERT: C  177 ASP cc_start: 0.8143 (t0) cc_final: 0.7906 (t0)
REVERT: D   49 LYS cc_start: 0.7031 (tmtt) cc_final: 0.6803 (mmmt)
REVERT: D   60 GLU cc_start: 0.8421 (tt0) cc_final: 0.8141 (tt0)
REVERT: D   87 TYR cc_start: 0.8965 (m-80) cc_final: 0.8618 (m-80)
REVERT: D  100 LYS cc_start: 0.8540 (mtmt) cc_final: 0.7864 (tttp)
REVERT: D  101 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8462 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7936 (mt-10)
REVERT: E    6 ASN cc_start: 0.8477 (t0) cc_final: 0.8240 (t0)
REVERT: E   84 ASP cc_start: 0.8801 (m-30) cc_final: 0.8432 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 212
  average time/residue: 0.2231
  time to fit residues: 60.8419
Evaluate side-chains
  190 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   99 ARG
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 73 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
A 184 ASN
B   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.121052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.096170 restraints weight = 9189.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.01
r_work: 0.2869 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7485  Z= 0.130
  Angle     :  0.488   8.550  10080  Z= 0.266
  Chirality :  0.037   0.166   1190
  Planarity :  0.003   0.030   1260
  Dihedral  :  3.304  13.395    980
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.78 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.28), residues: 910
  helix:  2.39 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.85 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  47 
 HIS   0.001   0.000   HIS E 118 
 PHE   0.005   0.001   PHE B  10 
 TYR   0.017   0.002   TYR E  61 
 ARG   0.003   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03991 (  455)
  hydrogen bonds       : angle       3.90615 ( 1350)
  covalent geometry    : bond        0.00296 ( 7485)
  covalent geometry    : angle       0.48846 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8528 (t0) cc_final: 0.8282 (t0)
REVERT: A   48 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7851 (mtmm)
REVERT: A   60 GLU cc_start: 0.8832 (tt0) cc_final: 0.8588 (tt0)
REVERT: A  100 LYS cc_start: 0.8778 (mtmt) cc_final: 0.7894 (ttpt)
REVERT: A  164 GLU cc_start: 0.8543 (mp0) cc_final: 0.8295 (mp0)
REVERT: A  165 ASN cc_start: 0.8971 (t0) cc_final: 0.8603 (t0)
REVERT: B   39 MET cc_start: 0.7967 (tpt) cc_final: 0.7488 (mmm)
REVERT: B   44 ASP cc_start: 0.7387 (t70) cc_final: 0.6986 (p0)
REVERT: B   77 ARG cc_start: 0.8368 (ttt180) cc_final: 0.8042 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7372 (ttpp)
REVERT: B  111 MET cc_start: 0.8238 (ttm) cc_final: 0.7841 (ttp)
REVERT: C  100 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7768 (ttmm)
REVERT: C  122 GLU cc_start: 0.8714 (tt0) cc_final: 0.8415 (mt-10)
REVERT: C  159 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8324 (mt-10)
REVERT: C  165 ASN cc_start: 0.9099 (t0) cc_final: 0.8753 (t0)
REVERT: C  177 ASP cc_start: 0.8175 (t0) cc_final: 0.7934 (t0)
REVERT: D   49 LYS cc_start: 0.7051 (tmtt) cc_final: 0.6830 (mmmt)
REVERT: D   60 GLU cc_start: 0.8386 (tt0) cc_final: 0.8103 (tt0)
REVERT: D  100 LYS cc_start: 0.8563 (mtmt) cc_final: 0.7917 (tttp)
REVERT: D  101 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8481 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7774 (mt-10)
REVERT: E    6 ASN cc_start: 0.8482 (t0) cc_final: 0.8207 (t0)
REVERT: E   84 ASP cc_start: 0.8800 (m-30) cc_final: 0.8441 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 197
  average time/residue: 0.2262
  time to fit residues: 56.7121
Evaluate side-chains
  194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue   99 ARG
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 11 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0170
   chunk 73 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0670
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN
E 184 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.121990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.097877 restraints weight = 9147.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.97
r_work: 0.2871 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7485  Z= 0.108
  Angle     :  0.470   8.308  10080  Z= 0.260
  Chirality :  0.035   0.167   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.214  14.031    980
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.24 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.93 (0.28), residues: 910
  helix:  2.49 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.85 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  18 
 HIS   0.001   0.000   HIS E 118 
 PHE   0.006   0.001   PHE E  20 
 TYR   0.030   0.002   TYR D  87 
 ARG   0.003   0.000   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  455)
  hydrogen bonds       : angle       3.82233 ( 1350)
  covalent geometry    : bond        0.00230 ( 7485)
  covalent geometry    : angle       0.46976 (10080)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8558 (t0) cc_final: 0.8326 (t0)
REVERT: A   48 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7789 (mtmm)
REVERT: A   60 GLU cc_start: 0.8806 (tt0) cc_final: 0.8548 (tt0)
REVERT: A  100 LYS cc_start: 0.8724 (mtmt) cc_final: 0.7858 (ttpt)
REVERT: A  164 GLU cc_start: 0.8408 (mp0) cc_final: 0.8135 (mp0)
REVERT: A  165 ASN cc_start: 0.8917 (t0) cc_final: 0.8625 (t0)
REVERT: B   39 MET cc_start: 0.7907 (tpt) cc_final: 0.7436 (mmm)
REVERT: B   44 ASP cc_start: 0.7316 (t70) cc_final: 0.6885 (p0)
REVERT: B   77 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7934 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7283 (ttpp)
REVERT: B  111 MET cc_start: 0.8144 (ttm) cc_final: 0.7763 (ttp)
REVERT: C  100 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7737 (ttmm)
REVERT: C  159 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: C  165 ASN cc_start: 0.9085 (t0) cc_final: 0.8794 (t0)
REVERT: C  177 ASP cc_start: 0.8113 (t0) cc_final: 0.7847 (t0)
REVERT: D    8 LYS cc_start: 0.9018 (tttm) cc_final: 0.8439 (ttmm)
REVERT: D   49 LYS cc_start: 0.7024 (tmtt) cc_final: 0.6793 (mmmt)
REVERT: D   60 GLU cc_start: 0.8440 (tt0) cc_final: 0.8163 (tt0)
REVERT: D   87 TYR cc_start: 0.8933 (m-80) cc_final: 0.8678 (m-80)
REVERT: D  100 LYS cc_start: 0.8738 (mtmt) cc_final: 0.7973 (tttp)
REVERT: D  159 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: E    6 ASN cc_start: 0.8464 (t0) cc_final: 0.8061 (t0)
REVERT: E   60 GLU cc_start: 0.8390 (tt0) cc_final: 0.8002 (tt0)
REVERT: E   84 ASP cc_start: 0.8738 (m-30) cc_final: 0.8370 (m-30)
  outliers start: 16
  outliers final: 15
  residues processed: 188
  average time/residue: 0.2305
  time to fit residues: 55.8842
Evaluate side-chains
  191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 VAL
Chi-restraints excluded: chain A residue  186 HIS
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain D residue    6 ASN
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain D residue  186 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  167 THR
Chi-restraints excluded: chain E residue  179 GLU
Chi-restraints excluded: chain E residue  186 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 72 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0170
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
B   6 ASN
D   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.120862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.096961 restraints weight = 9073.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.91
r_work: 0.2884 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7485  Z= 0.138
  Angle     :  0.509   8.316  10080  Z= 0.276
  Chirality :  0.037   0.167   1190
  Planarity :  0.003   0.028   1260
  Dihedral  :  3.249  14.347    980
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.76 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.88 (0.28), residues: 910
  helix:  2.46 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.83 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.000   HIS C 118 
 PHE   0.004   0.001   PHE B 120 
 TYR   0.027   0.002   TYR D  87 
 ARG   0.003   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  455)
  hydrogen bonds       : angle       3.87870 ( 1350)
  covalent geometry    : bond        0.00315 ( 7485)
  covalent geometry    : angle       0.50880 (10080)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4445.54 seconds
wall clock time: 78 minutes 21.17 seconds (4701.17 seconds total)