Starting phenix.real_space_refine
on Wed Mar 12 04:58:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvw_43571/03_2025/8vvw_43571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvw_43571/03_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_43571/03_2025/8vvw_43571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvw_43571/03_2025/8vvw_43571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvw_43571/03_2025/8vvw_43571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvw_43571/03_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-5624/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: 6.06, per 1000 atoms: 0.82
  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: 1.92
  Conformation dependent library (CDL) restraints added in 1.8 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: 0.68
  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: 1.95

  Time building geometry restraints manager: 2.62 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: 0.09
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:             16.400
  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:          0.650
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.690
  Find NCS groups from input model:        0.160
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.090
-------------------------------------------------------------------------------
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= 0.163
  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 

*********************** 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  : 0.792 
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: 0.2400
  time to fit residues: 75.0272
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  : 0.914 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.096894 restraints weight = 8978.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.92
r_work: 0.2813 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2643 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
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= 0.213
  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 

*********************** 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  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7581 (mtmm)
REVERT: A   60 GLU cc_start: 0.8837 (tt0) cc_final: 0.8572 (tt0)
REVERT: A  165 ASN cc_start: 0.8952 (t0) cc_final: 0.8674 (t0)
REVERT: B   39 MET cc_start: 0.7836 (tpt) cc_final: 0.7431 (mmp)
REVERT: B   48 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7951 (mtmm)
REVERT: B   60 GLU cc_start: 0.8520 (tt0) cc_final: 0.8251 (tt0)
REVERT: B   77 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7686 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7055 (ttpp)
REVERT: B  111 MET cc_start: 0.8109 (ttm) cc_final: 0.7555 (ttp)
REVERT: C   42 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: C   51 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8062 (mm-30)
REVERT: C  100 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7523 (ttmm)
REVERT: C  122 GLU cc_start: 0.8693 (tt0) cc_final: 0.8277 (mt-10)
REVERT: C  159 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8105 (mt-10)
REVERT: C  166 LEU cc_start: 0.8681 (pt) cc_final: 0.8412 (pt)
REVERT: C  177 ASP cc_start: 0.8085 (t0) cc_final: 0.7763 (t0)
REVERT: C  180 ILE cc_start: 0.8524 (mt) cc_final: 0.8306 (mt)
REVERT: D   49 LYS cc_start: 0.6797 (tmtt) cc_final: 0.6405 (ttpp)
REVERT: D   77 ARG cc_start: 0.8304 (ttt180) cc_final: 0.8029 (ttt90)
REVERT: D  100 LYS cc_start: 0.8565 (mtmt) cc_final: 0.7662 (tttp)
REVERT: D  159 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: D  179 GLU cc_start: 0.8492 (tt0) cc_final: 0.8275 (tt0)
REVERT: E    6 ASN cc_start: 0.8611 (t0) cc_final: 0.8329 (t0)
REVERT: E   84 ASP cc_start: 0.8721 (m-30) cc_final: 0.8254 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 214
  average time/residue: 0.2465
  time to fit residues: 68.7300
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  : 0.807 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   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 = 0.3274 r_free = 0.3274 target = 0.121231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.096384 restraints weight = 9138.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.98
r_work: 0.2841 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2148

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= 0.203
  Angle     :  0.472   7.744  10080  Z= 0.255
  Chirality :  0.036   0.143   1190
  Planarity :  0.003   0.024   1260
  Dihedral  :  3.341  15.059    980
  Min Nonbonded Distance : 2.465

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:  2.87 (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   0.005   0.001   PHE D  10 
 TYR   0.018   0.002   TYR E  61 
 ARG   0.003   0.000   ARG B  89 

*********************** 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
  206 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 189
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8291 (t0) cc_final: 0.8072 (t0)
REVERT: A   48 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7631 (mtmm)
REVERT: A   60 GLU cc_start: 0.8766 (tt0) cc_final: 0.8563 (tt0)
REVERT: A  164 GLU cc_start: 0.8518 (mp0) cc_final: 0.8119 (mp0)
REVERT: A  165 ASN cc_start: 0.8904 (t0) cc_final: 0.8474 (t0)
REVERT: B   39 MET cc_start: 0.7787 (tpt) cc_final: 0.7388 (mmp)
REVERT: B   77 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7766 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7110 (ttpp)
REVERT: B  111 MET cc_start: 0.8211 (ttm) cc_final: 0.7630 (ttp)
REVERT: C  100 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7469 (ttmm)
REVERT: C  122 GLU cc_start: 0.8706 (tt0) cc_final: 0.8329 (mt-10)
REVERT: C  159 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8201 (mt-10)
REVERT: C  165 ASN cc_start: 0.8986 (t0) cc_final: 0.8777 (t0)
REVERT: C  166 LEU cc_start: 0.8729 (pt) cc_final: 0.8439 (pt)
REVERT: C  177 ASP cc_start: 0.8063 (t0) cc_final: 0.7728 (t0)
REVERT: C  180 ILE cc_start: 0.8500 (mt) cc_final: 0.8288 (mt)
REVERT: D   49 LYS cc_start: 0.6809 (tmtt) cc_final: 0.6498 (mmmt)
REVERT: D  100 LYS cc_start: 0.8604 (mtmt) cc_final: 0.7680 (tttp)
REVERT: D  159 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8012 (mt-10)
REVERT: D  179 GLU cc_start: 0.8446 (tt0) cc_final: 0.8121 (tt0)
REVERT: E    6 ASN cc_start: 0.8610 (t0) cc_final: 0.8290 (t0)
REVERT: E   84 ASP cc_start: 0.8802 (m-30) cc_final: 0.8263 (m-30)
REVERT: E  159 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8385 (mt-10)
  outliers start: 17
  outliers final: 8
  residues processed: 204
  average time/residue: 0.3456
  time to fit residues: 91.1155
Evaluate side-chains
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 178
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0170
   chunk 42 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3266 r_free = 0.3266 target = 0.120843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.096274 restraints weight = 9066.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.95
r_work: 0.2843 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7485  Z= 0.189
  Angle     :  0.461   7.869  10080  Z= 0.249
  Chirality :  0.036   0.140   1190
  Planarity :  0.002   0.027   1260
  Dihedral  :  3.311  14.663    980
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.98 %
    Favored  : 87.07 %
  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:  2.43 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.97 (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   0.015   0.002   TYR D  87 
 ARG   0.002   0.000   ARG D   5 

*********************** 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
  215 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8504 (t0) cc_final: 0.8284 (t0)
REVERT: A   48 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7630 (mtmm)
REVERT: A   60 GLU cc_start: 0.8781 (tt0) cc_final: 0.8558 (tt0)
REVERT: A  164 GLU cc_start: 0.8535 (mp0) cc_final: 0.8168 (mp0)
REVERT: A  165 ASN cc_start: 0.8890 (t0) cc_final: 0.8551 (t0)
REVERT: B   39 MET cc_start: 0.7770 (tpt) cc_final: 0.7390 (mmp)
REVERT: B   77 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7790 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7118 (ttpp)
REVERT: B  111 MET cc_start: 0.8109 (ttm) cc_final: 0.7707 (ttp)
REVERT: C   42 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: C   51 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8107 (mm-30)
REVERT: C  100 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7481 (ttmm)
REVERT: C  122 GLU cc_start: 0.8711 (tt0) cc_final: 0.8338 (mt-10)
REVERT: C  159 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: C  165 ASN cc_start: 0.8963 (t0) cc_final: 0.8686 (t0)
REVERT: C  177 ASP cc_start: 0.8061 (t0) cc_final: 0.7739 (t0)
REVERT: D   49 LYS cc_start: 0.6846 (tmtt) cc_final: 0.6536 (mmmt)
REVERT: D   60 GLU cc_start: 0.8438 (tt0) cc_final: 0.8058 (tt0)
REVERT: D   87 TYR cc_start: 0.9007 (m-80) cc_final: 0.8772 (m-80)
REVERT: D  100 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7698 (tttp)
REVERT: D  159 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: E    6 ASN cc_start: 0.8571 (t0) cc_final: 0.8171 (t0)
REVERT: E   84 ASP cc_start: 0.8799 (m-30) cc_final: 0.8406 (m-30)
  outliers start: 16
  outliers final: 8
  residues processed: 211
  average time/residue: 0.2164
  time to fit residues: 59.2280
Evaluate side-chains
  196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 188
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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    6 ASN
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:    0.0770
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3265 r_free = 0.3265 target = 0.120836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.096520 restraints weight = 9031.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.94
r_work: 0.2864 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7485  Z= 0.182
  Angle     :  0.458   7.978  10080  Z= 0.249
  Chirality :  0.036   0.142   1190
  Planarity :  0.002   0.029   1260
  Dihedral  :  3.290  13.819    980
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.34 %
    Favored  : 86.46 %
  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:  2.46 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.93 (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   0.015   0.002   TYR C  61 
 ARG   0.002   0.000   ARG D  89 

*********************** 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
  209 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7792 (mtmm)
REVERT: A  164 GLU cc_start: 0.8496 (mp0) cc_final: 0.8208 (mp0)
REVERT: A  165 ASN cc_start: 0.8880 (t0) cc_final: 0.8519 (t0)
REVERT: B   39 MET cc_start: 0.7764 (tpt) cc_final: 0.7475 (mmm)
REVERT: B   77 ARG cc_start: 0.8448 (ttt180) cc_final: 0.7956 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7360 (ttpp)
REVERT: B  111 MET cc_start: 0.8194 (ttm) cc_final: 0.7804 (ttp)
REVERT: C  100 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7709 (ttmm)
REVERT: C  122 GLU cc_start: 0.8645 (tt0) cc_final: 0.8399 (mt-10)
REVERT: C  159 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: C  165 ASN cc_start: 0.8949 (t0) cc_final: 0.8603 (t0)
REVERT: C  177 ASP cc_start: 0.8118 (t0) cc_final: 0.7879 (t0)
REVERT: D   49 LYS cc_start: 0.6992 (tmtt) cc_final: 0.6754 (mmmt)
REVERT: D   60 GLU cc_start: 0.8446 (tt0) cc_final: 0.8113 (tt0)
REVERT: D   87 TYR cc_start: 0.9024 (m-80) cc_final: 0.8777 (m-80)
REVERT: D  100 LYS cc_start: 0.8694 (mtmt) cc_final: 0.7933 (tttp)
REVERT: D  159 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: E    6 ASN cc_start: 0.8542 (t0) cc_final: 0.8162 (t0)
REVERT: E   84 ASP cc_start: 0.8802 (m-30) cc_final: 0.8427 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 205
  average time/residue: 0.2486
  time to fit residues: 65.9306
Evaluate side-chains
  181 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
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  167 THR
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0670
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0470
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.4016

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.121066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097222 restraints weight = 9137.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.90
r_work: 0.2918 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7485  Z= 0.151
  Angle     :  0.447   8.085  10080  Z= 0.245
  Chirality :  0.035   0.148   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.262  13.020    980
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.29 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.94 (0.28), residues: 910
  helix:  2.49 (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  18 
 HIS   0.002   0.000   HIS E 118 
 PHE   0.005   0.001   PHE B  20 
 TYR   0.017   0.002   TYR E  61 
 ARG   0.002   0.000   ARG D 174 

*********************** 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
  199 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 1.262 
Fit side-chains
REVERT: A   48 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7745 (mtmm)
REVERT: A  164 GLU cc_start: 0.8504 (mp0) cc_final: 0.8219 (mp0)
REVERT: A  165 ASN cc_start: 0.8887 (t0) cc_final: 0.8554 (t0)
REVERT: B   39 MET cc_start: 0.7871 (tpt) cc_final: 0.7454 (mmm)
REVERT: B   44 ASP cc_start: 0.7380 (t70) cc_final: 0.6988 (p0)
REVERT: B   45 ASP cc_start: 0.7719 (t0) cc_final: 0.7443 (t0)
REVERT: B   77 ARG cc_start: 0.8276 (ttt180) cc_final: 0.7936 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7223 (ttpp)
REVERT: B  111 MET cc_start: 0.8091 (ttm) cc_final: 0.7715 (ttp)
REVERT: C  100 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7625 (ttmm)
REVERT: C  122 GLU cc_start: 0.8604 (tt0) cc_final: 0.8378 (mt-10)
REVERT: C  159 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8245 (mt-10)
REVERT: C  165 ASN cc_start: 0.9031 (t0) cc_final: 0.8622 (t0)
REVERT: C  177 ASP cc_start: 0.8064 (t0) cc_final: 0.7806 (t0)
REVERT: D   49 LYS cc_start: 0.6947 (tmtt) cc_final: 0.6709 (mmmt)
REVERT: D   60 GLU cc_start: 0.8382 (tt0) cc_final: 0.8043 (tt0)
REVERT: D  100 LYS cc_start: 0.8653 (mtmt) cc_final: 0.7915 (tttp)
REVERT: D  159 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7963 (mt-10)
REVERT: E    6 ASN cc_start: 0.8511 (t0) cc_final: 0.8140 (t0)
REVERT: E   39 MET cc_start: 0.7792 (tpp) cc_final: 0.7576 (tpp)
REVERT: E   84 ASP cc_start: 0.8772 (m-30) cc_final: 0.8389 (m-30)
REVERT: E  159 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8083 (mp0)
  outliers start: 18
  outliers final: 16
  residues processed: 196
  average time/residue: 0.2862
  time to fit residues: 72.3400
Evaluate side-chains
  196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain A residue   31 VAL
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  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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0370
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.6462

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.126094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.102012 restraints weight = 8935.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.91
r_work: 0.2797 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2630 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7485  Z= 0.197
  Angle     :  0.470   8.327  10080  Z= 0.254
  Chirality :  0.036   0.155   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.284  13.588    980
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.41 %
    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:  2.85 (0.28), residues: 910
  helix:  2.41 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.88 (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   0.004   0.001   PHE B  10 
 TYR   0.022   0.002   TYR D  87 
 ARG   0.002   0.000   ARG D 174 

*********************** 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
  206 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8400 (t0) cc_final: 0.8109 (t0)
REVERT: A   48 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7750 (mtmm)
REVERT: A  100 LYS cc_start: 0.8704 (mtmt) cc_final: 0.7746 (ttpt)
REVERT: A  164 GLU cc_start: 0.8553 (mp0) cc_final: 0.8267 (mp0)
REVERT: A  165 ASN cc_start: 0.8908 (t0) cc_final: 0.8535 (t0)
REVERT: B   39 MET cc_start: 0.7935 (tpt) cc_final: 0.7496 (mmm)
REVERT: B   44 ASP cc_start: 0.7335 (t70) cc_final: 0.6939 (p0)
REVERT: B   77 ARG cc_start: 0.8302 (ttt180) cc_final: 0.7809 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7266 (ttpp)
REVERT: B  111 MET cc_start: 0.8101 (ttm) cc_final: 0.7710 (ttp)
REVERT: C  100 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7610 (ttmm)
REVERT: C  122 GLU cc_start: 0.8684 (tt0) cc_final: 0.8349 (mt-10)
REVERT: C  159 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: C  165 ASN cc_start: 0.9024 (t0) cc_final: 0.8640 (t0)
REVERT: C  177 ASP cc_start: 0.8080 (t0) cc_final: 0.7811 (t0)
REVERT: D   49 LYS cc_start: 0.6986 (tmtt) cc_final: 0.6754 (mmmt)
REVERT: D   60 GLU cc_start: 0.8446 (tt0) cc_final: 0.8065 (tt0)
REVERT: D   87 TYR cc_start: 0.9004 (m-80) cc_final: 0.8720 (m-80)
REVERT: D  100 LYS cc_start: 0.8735 (mtmt) cc_final: 0.7894 (tttp)
REVERT: D  101 ARG cc_start: 0.8666 (ttm170) cc_final: 0.8410 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7782 (mt-10)
REVERT: E    6 ASN cc_start: 0.8528 (t0) cc_final: 0.8100 (t0)
REVERT: E   84 ASP cc_start: 0.8798 (m-30) cc_final: 0.8404 (m-30)
  outliers start: 19
  outliers final: 15
  residues processed: 200
  average time/residue: 0.2618
  time to fit residues: 67.6403
Evaluate side-chains
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0270
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.7042

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.129483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.105625 restraints weight = 8891.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.89
r_work: 0.2868 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2663

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= 0.211
  Angle     :  0.485   8.330  10080  Z= 0.262
  Chirality :  0.037   0.161   1190
  Planarity :  0.003   0.032   1260
  Dihedral  :  3.310  13.577    980
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.78 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.28), residues: 910
  helix:  2.39 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.88 (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   0.004   0.001   PHE B 120 
 TYR   0.023   0.002   TYR D  87 
 ARG   0.002   0.000   ARG D  89 

*********************** 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
  198 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8475 (t0) cc_final: 0.8162 (t0)
REVERT: A   48 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7801 (mtmm)
REVERT: A  100 LYS cc_start: 0.8753 (mtmt) cc_final: 0.7834 (ttpt)
REVERT: A  164 GLU cc_start: 0.8532 (mp0) cc_final: 0.8269 (mp0)
REVERT: A  165 ASN cc_start: 0.8924 (t0) cc_final: 0.8577 (t0)
REVERT: B   39 MET cc_start: 0.7890 (tpt) cc_final: 0.7454 (mmm)
REVERT: B   44 ASP cc_start: 0.7363 (t70) cc_final: 0.6981 (p0)
REVERT: B   77 ARG cc_start: 0.8331 (ttt180) cc_final: 0.7995 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7300 (ttpp)
REVERT: B  111 MET cc_start: 0.8209 (ttm) cc_final: 0.7788 (ttp)
REVERT: C  100 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7717 (ttmm)
REVERT: C  122 GLU cc_start: 0.8679 (tt0) cc_final: 0.8381 (mt-10)
REVERT: C  159 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8317 (mt-10)
REVERT: C  165 ASN cc_start: 0.9029 (t0) cc_final: 0.8678 (t0)
REVERT: C  177 ASP cc_start: 0.8158 (t0) cc_final: 0.7900 (t0)
REVERT: C  182 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: D   49 LYS cc_start: 0.7016 (tmtt) cc_final: 0.6795 (mmmt)
REVERT: D   60 GLU cc_start: 0.8383 (tt0) cc_final: 0.8040 (tt0)
REVERT: D   87 TYR cc_start: 0.8952 (m-80) cc_final: 0.8644 (m-80)
REVERT: D  100 LYS cc_start: 0.8762 (mtmt) cc_final: 0.7970 (tttp)
REVERT: D  101 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8453 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: E    6 ASN cc_start: 0.8555 (t0) cc_final: 0.8104 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 193
  average time/residue: 0.2531
  time to fit residues: 62.0863
Evaluate side-chains
  196 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
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   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  167 THR
Chi-restraints excluded: chain C residue  182 ILE
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   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:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.1980
   chunk 53 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3273 r_free = 0.3273 target = 0.121011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.096953 restraints weight = 9216.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.93
r_work: 0.2817 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2740

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= 0.201
  Angle     :  0.485   8.446  10080  Z= 0.262
  Chirality :  0.036   0.167   1190
  Planarity :  0.003   0.030   1260
  Dihedral  :  3.315  14.116    980
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.02 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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   0.004   0.001   PHE B 120 
 TYR   0.022   0.002   TYR D  87 
 ARG   0.003   0.000   ARG C  89 

*********************** 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
  208 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8480 (t0) cc_final: 0.8221 (t0)
REVERT: A   48 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7691 (mtmm)
REVERT: A  100 LYS cc_start: 0.8649 (mtmt) cc_final: 0.7656 (ttpt)
REVERT: A  164 GLU cc_start: 0.8594 (mp0) cc_final: 0.8290 (mp0)
REVERT: A  165 ASN cc_start: 0.8889 (t0) cc_final: 0.8557 (t0)
REVERT: B   39 MET cc_start: 0.7889 (tpt) cc_final: 0.7427 (mmm)
REVERT: B   44 ASP cc_start: 0.7314 (t70) cc_final: 0.6891 (p0)
REVERT: B   77 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7822 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7111 (ttpp)
REVERT: B  111 MET cc_start: 0.8150 (ttm) cc_final: 0.7723 (ttp)
REVERT: C  100 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7536 (ttmm)
REVERT: C  122 GLU cc_start: 0.8635 (tt0) cc_final: 0.8283 (mt-10)
REVERT: C  159 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8306 (mt-10)
REVERT: C  165 ASN cc_start: 0.9108 (t0) cc_final: 0.8732 (t0)
REVERT: C  177 ASP cc_start: 0.8047 (t0) cc_final: 0.7801 (t0)
REVERT: D   49 LYS cc_start: 0.6897 (tmtt) cc_final: 0.6648 (mmmt)
REVERT: D   60 GLU cc_start: 0.8409 (tt0) cc_final: 0.8075 (tt0)
REVERT: D   87 TYR cc_start: 0.9015 (m-80) cc_final: 0.8647 (m-80)
REVERT: D  100 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7657 (tttp)
REVERT: D  101 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8351 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7767 (mt-10)
REVERT: E    6 ASN cc_start: 0.8468 (t0) cc_final: 0.8196 (t0)
REVERT: E  179 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8219 (pt0)
  outliers start: 20
  outliers final: 16
  residues processed: 205
  average time/residue: 0.2288
  time to fit residues: 60.6178
Evaluate side-chains
  195 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASN
Chi-restraints excluded: chain A residue   31 VAL
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  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   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:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.122953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.099098 restraints weight = 9120.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.90
r_work: 0.2828 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2775

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= 0.204
  Angle     :  0.499   8.414  10080  Z= 0.271
  Chirality :  0.037   0.171   1190
  Planarity :  0.003   0.029   1260
  Dihedral  :  3.357  15.855    980
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.63 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.28), residues: 910
  helix:  2.38 (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   0.004   0.001   PHE B 120 
 TYR   0.021   0.002   TYR D  87 
 ARG   0.003   0.000   ARG C  89 

********************** 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
  200 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 182
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8495 (t0) cc_final: 0.8223 (t0)
REVERT: A   48 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7675 (mtmm)
REVERT: A   60 GLU cc_start: 0.8388 (tt0) cc_final: 0.8164 (tp30)
REVERT: A  100 LYS cc_start: 0.8629 (mtmt) cc_final: 0.7630 (ttpt)
REVERT: A  164 GLU cc_start: 0.8576 (mp0) cc_final: 0.8270 (mp0)
REVERT: A  165 ASN cc_start: 0.8920 (t0) cc_final: 0.8557 (t0)
REVERT: B   39 MET cc_start: 0.7885 (tpt) cc_final: 0.7422 (mmm)
REVERT: B   44 ASP cc_start: 0.7295 (t70) cc_final: 0.6865 (p0)
REVERT: B   77 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7797 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7079 (ttpp)
REVERT: B  111 MET cc_start: 0.8142 (ttm) cc_final: 0.7705 (ttp)
REVERT: C  100 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7509 (ttmm)
REVERT: C  122 GLU cc_start: 0.8616 (tt0) cc_final: 0.8263 (mt-10)
REVERT: C  159 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8310 (mt-10)
REVERT: C  165 ASN cc_start: 0.9102 (t0) cc_final: 0.8751 (t0)
REVERT: C  177 ASP cc_start: 0.8169 (t0) cc_final: 0.7918 (t0)
REVERT: D   49 LYS cc_start: 0.6895 (tmtt) cc_final: 0.6628 (mmmt)
REVERT: D   60 GLU cc_start: 0.8381 (tt0) cc_final: 0.8047 (tt0)
REVERT: D   87 TYR cc_start: 0.9001 (m-80) cc_final: 0.8620 (m-80)
REVERT: D  100 LYS cc_start: 0.8446 (mtmt) cc_final: 0.7635 (tttp)
REVERT: D  101 ARG cc_start: 0.8597 (ttm170) cc_final: 0.8333 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: E    6 ASN cc_start: 0.8471 (t0) cc_final: 0.8180 (t0)
REVERT: E   84 ASP cc_start: 0.8775 (m-30) cc_final: 0.8368 (m-30)
  outliers start: 18
  outliers final: 16
  residues processed: 196
  average time/residue: 0.2230
  time to fit residues: 55.8983
Evaluate side-chains
  193 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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   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 84 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0470
   chunk 59 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.4476

-------------------------------------------------------------------------------
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 = 0.3321 r_free = 0.3321 target = 0.124530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.100175 restraints weight = 8986.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 1.98
r_work: 0.2815 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
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      :  0.003   0.037   7485  Z= 0.173
  Angle     :  0.489   8.425  10080  Z= 0.268
  Chirality :  0.036   0.168   1190
  Planarity :  0.003   0.028   1260
  Dihedral  :  3.326  15.128    980
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.76 %
    Favored  : 82.93 %
  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:  2.83 (0.28), residues: 910
  helix:  2.42 (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 A  18 
 HIS   0.001   0.000   HIS E 118 
 PHE   0.005   0.001   PHE E  20 
 TYR   0.022   0.002   TYR D  87 
 ARG   0.003   0.000   ARG C  89 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4642.85 seconds
wall clock time: 84 minutes 24.42 seconds (5064.42 seconds total)