Starting phenix.real_space_refine
on Wed Sep 17 08:46:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvw_43571/09_2025/8vvw_43571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvw_43571/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvw_43571/09_2025/8vvw_43571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvw_43571/09_2025/8vvw_43571.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvw_43571/09_2025/8vvw_43571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvw_43571/09_2025/8vvw_43571.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 1.34, per 1000 atoms: 0.18
  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: 0.57
  Conformation dependent library (CDL) restraints added in 412.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 1.06

  Time building geometry restraints manager: 0.79 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             11.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     7.880
  Find NCS groups from input model:        0.070
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.880
-------------------------------------------------------------------------------
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 : 5.41
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG C 101 
 TYR   0.013   0.002   TYR A  61 
 PHE   0.002   0.001   PHE D  10 
 TRP   0.002   0.000   TRP A  18 
 HIS   0.001   0.000   HIS A 116 

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

*********************** 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  : 0.281 
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: 0.7769 (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: 0.7695 (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: 0.7485 (mmp)
REVERT: B   48 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8032 (mtmm)
REVERT: B   49 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7549 (ttpp)
REVERT: B   77 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7849 (ttm-80)
REVERT: B  100 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7538 (ttpp)
REVERT: B  111 MET cc_start: 0.7941 (ttm) cc_final: 0.7602 (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: 0.7834 (mm-30)
REVERT: C   74 ILE cc_start: 0.8737 (pt) cc_final: 0.8518 (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: 0.7847 (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: 0.7881 (mt-10)
REVERT: C  177 ASP cc_start: 0.7849 (t0) cc_final: 0.7636 (t0)
REVERT: D   49 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6885 (mmmt)
REVERT: D   51 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8076 (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: 0.8118 (ttp)
REVERT: D  121 ASP cc_start: 0.8167 (m-30) cc_final: 0.7943 (m-30)
REVERT: D  159 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7564 (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: 0.7769 (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: 0.1078
  time to fit residues: 33.7227
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  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3264 r_free = 0.3264 target = 0.120847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.096175 restraints weight = 9121.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.94
r_work: 0.2886 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7485  Z= 0.152
  Angle     :  0.494   7.635  10080  Z= 0.265
  Chirality :  0.037   0.137   1190
  Planarity :  0.003   0.019   1260
  Dihedral  :  3.330  15.629    980
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.78 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.28), residues: 910
  helix:  2.31 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.96 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  89 
 TYR   0.017   0.002   TYR D  61 
 PHE   0.005   0.001   PHE D  10 
 TRP   0.005   0.001   TRP C  18 
 HIS   0.002   0.000   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7485)
  covalent geometry    : angle       0.49423 (10080)
  hydrogen bonds       : bond        0.04354 (  455)
  hydrogen bonds       : angle       3.97158 ( 1350)

*********************** 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
  212 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 205
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8767 (mttt) cc_final: 0.8554 (mttm)
REVERT: A   48 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7656 (mtmm)
REVERT: A   60 GLU cc_start: 0.8808 (tt0) cc_final: 0.8556 (tt0)
REVERT: A  165 ASN cc_start: 0.9014 (t0) cc_final: 0.8811 (t0)
REVERT: B   39 MET cc_start: 0.7836 (tpt) cc_final: 0.7460 (mmp)
REVERT: B   48 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8107 (mtmm)
REVERT: B   49 LYS cc_start: 0.7567 (tmtt) cc_final: 0.7312 (ttpp)
REVERT: B   60 GLU cc_start: 0.8499 (tt0) cc_final: 0.8260 (tt0)
REVERT: B   77 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7863 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7165 (ttpp)
REVERT: B  111 MET cc_start: 0.8122 (ttm) cc_final: 0.7585 (ttp)
REVERT: C  100 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7567 (ttmm)
REVERT: C  122 GLU cc_start: 0.8667 (tt0) cc_final: 0.8302 (mt-10)
REVERT: C  159 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: C  166 LEU cc_start: 0.8770 (pt) cc_final: 0.8507 (pt)
REVERT: C  177 ASP cc_start: 0.8112 (t0) cc_final: 0.7799 (t0)
REVERT: C  180 ILE cc_start: 0.8586 (mt) cc_final: 0.8374 (mt)
REVERT: D   49 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6501 (ttpp)
REVERT: D   77 ARG cc_start: 0.8336 (ttt180) cc_final: 0.8079 (ttt90)
REVERT: D  100 LYS cc_start: 0.8611 (mtmt) cc_final: 0.7773 (tttp)
REVERT: D  159 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7955 (mt-10)
REVERT: E    6 ASN cc_start: 0.8576 (t0) cc_final: 0.8268 (t0)
REVERT: E   84 ASP cc_start: 0.8745 (m-30) cc_final: 0.8305 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 210
  average time/residue: 0.0915
  time to fit residues: 25.2410
Evaluate side-chains
  185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 181
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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 36 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.121299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.097810 restraints weight = 9031.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.79
r_work: 0.2845 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7485  Z= 0.150
  Angle     :  0.484   7.841  10080  Z= 0.260
  Chirality :  0.037   0.145   1190
  Planarity :  0.003   0.023   1260
  Dihedral  :  3.381  15.846    980
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.49 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.28), residues: 910
  helix:  2.37 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.91 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.018   0.002   TYR E  61 
 PHE   0.005   0.001   PHE D  10 
 TRP   0.003   0.001   TRP E  47 
 HIS   0.002   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7485)
  covalent geometry    : angle       0.48369 (10080)
  hydrogen bonds       : bond        0.04290 (  455)
  hydrogen bonds       : angle       3.89847 ( 1350)

*********************** 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
  194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8297 (t0) cc_final: 0.8076 (t0)
REVERT: A   48 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7637 (mtmm)
REVERT: A   60 GLU cc_start: 0.8734 (tt0) cc_final: 0.8432 (tt0)
REVERT: A  164 GLU cc_start: 0.8533 (mp0) cc_final: 0.8141 (mp0)
REVERT: A  165 ASN cc_start: 0.8944 (t0) cc_final: 0.8599 (t0)
REVERT: B   39 MET cc_start: 0.7815 (tpt) cc_final: 0.7423 (mmp)
REVERT: B   48 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8268 (mtmm)
REVERT: B   49 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7245 (ttpp)
REVERT: B   77 ARG cc_start: 0.8242 (ttt180) cc_final: 0.7671 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7104 (ttpp)
REVERT: B  111 MET cc_start: 0.8228 (ttm) cc_final: 0.7692 (ttp)
REVERT: C  100 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7452 (ttmm)
REVERT: C  122 GLU cc_start: 0.8667 (tt0) cc_final: 0.8309 (mt-10)
REVERT: C  159 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8149 (mt-10)
REVERT: C  166 LEU cc_start: 0.8769 (pt) cc_final: 0.8466 (pt)
REVERT: C  177 ASP cc_start: 0.8002 (t0) cc_final: 0.7682 (t0)
REVERT: D   49 LYS cc_start: 0.6814 (tmtt) cc_final: 0.6563 (mmmt)
REVERT: D  100 LYS cc_start: 0.8590 (mtmt) cc_final: 0.7659 (tttp)
REVERT: D  159 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7947 (mt-10)
REVERT: E    6 ASN cc_start: 0.8617 (t0) cc_final: 0.8287 (t0)
REVERT: E   72 SER cc_start: 0.8550 (p) cc_final: 0.8228 (t)
REVERT: E   84 ASP cc_start: 0.8802 (m-30) cc_final: 0.8270 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 192
  average time/residue: 0.1063
  time to fit residues: 26.2874
Evaluate side-chains
  176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 170
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 25 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.121766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.097031 restraints weight = 9113.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.96
r_work: 0.2824 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7485  Z= 0.120
  Angle     :  0.451   7.907  10080  Z= 0.244
  Chirality :  0.035   0.139   1190
  Planarity :  0.002   0.026   1260
  Dihedral  :  3.329  14.992    980
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.14
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.92 (0.28), residues: 910
  helix:  2.46 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.92 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 TYR   0.015   0.002   TYR D  87 
 PHE   0.005   0.001   PHE B 120 
 TRP   0.003   0.001   TRP B  47 
 HIS   0.003   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7485)
  covalent geometry    : angle       0.45058 (10080)
  hydrogen bonds       : bond        0.04011 (  455)
  hydrogen bonds       : angle       3.81967 ( 1350)

*********************** 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
  197 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8526 (t0) cc_final: 0.8305 (t0)
REVERT: A   48 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7680 (mtmm)
REVERT: A   60 GLU cc_start: 0.8787 (tt0) cc_final: 0.8488 (tt0)
REVERT: A  164 GLU cc_start: 0.8609 (mp0) cc_final: 0.8254 (mp0)
REVERT: A  165 ASN cc_start: 0.8956 (t0) cc_final: 0.8526 (t0)
REVERT: B   39 MET cc_start: 0.7815 (tpt) cc_final: 0.7485 (mmm)
REVERT: B   48 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8288 (mtmm)
REVERT: B   77 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7908 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7116 (ttpp)
REVERT: B  111 MET cc_start: 0.8134 (ttm) cc_final: 0.7757 (ttp)
REVERT: B  121 ASP cc_start: 0.8204 (m-30) cc_final: 0.7924 (m-30)
REVERT: C  100 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7501 (ttmm)
REVERT: C  122 GLU cc_start: 0.8717 (tt0) cc_final: 0.8344 (mt-10)
REVERT: C  159 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: C  177 ASP cc_start: 0.8056 (t0) cc_final: 0.7814 (t0)
REVERT: D   49 LYS cc_start: 0.6870 (tmtt) cc_final: 0.6567 (mmmt)
REVERT: D   60 GLU cc_start: 0.8490 (tt0) cc_final: 0.8103 (tt0)
REVERT: D   87 TYR cc_start: 0.9042 (m-80) cc_final: 0.8780 (m-80)
REVERT: D  100 LYS cc_start: 0.8622 (mtmt) cc_final: 0.7720 (tttp)
REVERT: D  159 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: E    6 ASN cc_start: 0.8571 (t0) cc_final: 0.8168 (t0)
REVERT: E   84 ASP cc_start: 0.8812 (m-30) cc_final: 0.8448 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 193
  average time/residue: 0.1065
  time to fit residues: 26.6763
Evaluate side-chains
  182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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   44 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain D residue  167 THR
Chi-restraints excluded: chain E residue  167 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    0.0030
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.3790

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.122423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.099622 restraints weight = 9092.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.75
r_work: 0.2951 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7485  Z= 0.102
  Angle     :  0.433   7.715  10080  Z= 0.238
  Chirality :  0.035   0.139   1190
  Planarity :  0.002   0.029   1260
  Dihedral  :  3.272  13.636    980
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.28), residues: 910
  helix:  2.56 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.94 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 TYR   0.016   0.002   TYR D  87 
 PHE   0.005   0.001   PHE B 120 
 TRP   0.003   0.001   TRP B  47 
 HIS   0.002   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 7485)
  covalent geometry    : angle       0.43328 (10080)
  hydrogen bonds       : bond        0.03763 (  455)
  hydrogen bonds       : angle       3.79547 ( 1350)

*********************** 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
  199 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8392 (t0) cc_final: 0.8190 (t0)
REVERT: A   48 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7666 (mtmm)
REVERT: A   60 GLU cc_start: 0.8680 (tt0) cc_final: 0.8368 (tt0)
REVERT: A  164 GLU cc_start: 0.8534 (mp0) cc_final: 0.8214 (mp0)
REVERT: A  165 ASN cc_start: 0.8929 (t0) cc_final: 0.8516 (t0)
REVERT: B   39 MET cc_start: 0.7762 (tpt) cc_final: 0.7428 (mmm)
REVERT: B   48 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8268 (mtmm)
REVERT: B   77 ARG cc_start: 0.8334 (ttt180) cc_final: 0.7799 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7130 (ttpp)
REVERT: B  111 MET cc_start: 0.8076 (ttm) cc_final: 0.7736 (ttp)
REVERT: B  121 ASP cc_start: 0.8182 (m-30) cc_final: 0.7893 (m-30)
REVERT: C  100 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7528 (ttmm)
REVERT: C  122 GLU cc_start: 0.8537 (tt0) cc_final: 0.8278 (mt-10)
REVERT: C  159 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: C  165 ASN cc_start: 0.8878 (t0) cc_final: 0.8676 (t0)
REVERT: C  177 ASP cc_start: 0.7996 (t0) cc_final: 0.7739 (t0)
REVERT: D   49 LYS cc_start: 0.6720 (tmtt) cc_final: 0.6485 (mmmt)
REVERT: D   60 GLU cc_start: 0.8396 (tt0) cc_final: 0.8036 (tt0)
REVERT: D  100 LYS cc_start: 0.8600 (mtmt) cc_final: 0.7739 (tttp)
REVERT: D  159 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7806 (mt-10)
REVERT: E    6 ASN cc_start: 0.8480 (t0) cc_final: 0.8129 (t0)
REVERT: E   84 ASP cc_start: 0.8769 (m-30) cc_final: 0.8408 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 195
  average time/residue: 0.1038
  time to fit residues: 26.2786
Evaluate side-chains
  176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  167 THR
Chi-restraints excluded: chain C residue   44 ASP
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  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  167 THR
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 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.120476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.096234 restraints weight = 9132.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.93
r_work: 0.2829 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2522

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= 0.137
  Angle     :  0.462   8.088  10080  Z= 0.248
  Chirality :  0.036   0.151   1190
  Planarity :  0.003   0.030   1260
  Dihedral  :  3.295  14.233    980
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.44 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.28), residues: 910
  helix:  2.46 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.88 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  89 
 TYR   0.021   0.002   TYR E  61 
 PHE   0.004   0.001   PHE B 120 
 TRP   0.003   0.001   TRP B  47 
 HIS   0.002   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7485)
  covalent geometry    : angle       0.46228 (10080)
  hydrogen bonds       : bond        0.04113 (  455)
  hydrogen bonds       : angle       3.80781 ( 1350)

*********************** 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
  191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8478 (t0) cc_final: 0.8223 (t0)
REVERT: A   48 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7697 (mtmm)
REVERT: A   60 GLU cc_start: 0.8777 (tt0) cc_final: 0.8466 (tt0)
REVERT: A  100 LYS cc_start: 0.8671 (mtmt) cc_final: 0.7710 (ttpt)
REVERT: A  164 GLU cc_start: 0.8573 (mp0) cc_final: 0.8221 (mp0)
REVERT: A  165 ASN cc_start: 0.8880 (t0) cc_final: 0.8609 (t0)
REVERT: B   39 MET cc_start: 0.7819 (tpt) cc_final: 0.7449 (mmm)
REVERT: B   48 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8237 (mtmm)
REVERT: B   77 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7894 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7159 (ttpp)
REVERT: B  111 MET cc_start: 0.8143 (ttm) cc_final: 0.7759 (ttp)
REVERT: C  100 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7535 (ttmm)
REVERT: C  122 GLU cc_start: 0.8566 (tt0) cc_final: 0.8259 (mt-10)
REVERT: C  159 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8232 (mt-10)
REVERT: C  165 ASN cc_start: 0.8829 (t0) cc_final: 0.8621 (t0)
REVERT: C  177 ASP cc_start: 0.8056 (t0) cc_final: 0.7786 (t0)
REVERT: C  182 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7827 (mp)
REVERT: D   49 LYS cc_start: 0.6893 (tmtt) cc_final: 0.6645 (mmmt)
REVERT: D   60 GLU cc_start: 0.8450 (tt0) cc_final: 0.8049 (tt0)
REVERT: D   87 TYR cc_start: 0.9079 (m-80) cc_final: 0.8765 (m-80)
REVERT: D  100 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7698 (tttp)
REVERT: D  101 ARG cc_start: 0.8635 (ttm170) cc_final: 0.8362 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7906 (mt-10)
REVERT: E    6 ASN cc_start: 0.8543 (t0) cc_final: 0.8106 (t0)
REVERT: E   84 ASP cc_start: 0.8814 (m-30) cc_final: 0.8420 (m-30)
REVERT: E  159 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7993 (mp0)
  outliers start: 22
  outliers final: 15
  residues processed: 186
  average time/residue: 0.1138
  time to fit residues: 26.8812
Evaluate side-chains
  181 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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   44 ASP
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  182 ILE
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  186 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 86 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   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
E 184 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.127767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.106385 restraints weight = 8995.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.61
r_work: 0.2932 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2615

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= 0.136
  Angle     :  0.468   8.342  10080  Z= 0.253
  Chirality :  0.037   0.157   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.299  13.836    980
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.28), residues: 910
  helix:  2.44 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.88 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  89 
 TYR   0.022   0.002   TYR D  87 
 PHE   0.004   0.001   PHE B 120 
 TRP   0.003   0.001   TRP B  47 
 HIS   0.001   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7485)
  covalent geometry    : angle       0.46807 (10080)
  hydrogen bonds       : bond        0.04090 (  455)
  hydrogen bonds       : angle       3.84978 ( 1350)

*********************** 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
  192 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8405 (t0) cc_final: 0.8161 (t0)
REVERT: A   48 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7798 (mtmm)
REVERT: A   60 GLU cc_start: 0.8669 (tt0) cc_final: 0.8335 (tt0)
REVERT: A  100 LYS cc_start: 0.8709 (mtmt) cc_final: 0.7777 (ttpt)
REVERT: A  164 GLU cc_start: 0.8508 (mp0) cc_final: 0.8227 (mp0)
REVERT: A  165 ASN cc_start: 0.8867 (t0) cc_final: 0.8636 (t0)
REVERT: B   39 MET cc_start: 0.7808 (tpt) cc_final: 0.7477 (mmm)
REVERT: B   48 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8317 (mtmm)
REVERT: B   77 ARG cc_start: 0.8372 (ttt180) cc_final: 0.8054 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7249 (ttpp)
REVERT: B  111 MET cc_start: 0.8214 (ttm) cc_final: 0.7813 (ttp)
REVERT: C  100 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7626 (ttmm)
REVERT: C  122 GLU cc_start: 0.8490 (tt0) cc_final: 0.8274 (mt-10)
REVERT: C  159 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8233 (mt-10)
REVERT: C  177 ASP cc_start: 0.7974 (t0) cc_final: 0.7723 (t0)
REVERT: C  182 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7982 (mp)
REVERT: D   60 GLU cc_start: 0.8311 (tt0) cc_final: 0.7951 (tt0)
REVERT: D   87 TYR cc_start: 0.9018 (m-80) cc_final: 0.8639 (m-80)
REVERT: D  100 LYS cc_start: 0.8638 (mtmt) cc_final: 0.7920 (tttp)
REVERT: D  101 ARG cc_start: 0.8666 (ttm170) cc_final: 0.8406 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7804 (mt-10)
REVERT: E    6 ASN cc_start: 0.8526 (t0) cc_final: 0.8093 (t0)
REVERT: E   84 ASP cc_start: 0.8773 (m-30) cc_final: 0.8392 (m-30)
  outliers start: 22
  outliers final: 15
  residues processed: 188
  average time/residue: 0.1102
  time to fit residues: 26.5300
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  : 0.345 
-------------------------------------------------------------------------------
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   44 ASP
Chi-restraints excluded: chain C residue   64 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  182 ILE
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  186 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3375 r_free = 0.3375 target = 0.128941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.106907 restraints weight = 9084.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.67
r_work: 0.2865 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7485  Z= 0.154
  Angle     :  0.492   8.525  10080  Z= 0.265
  Chirality :  0.037   0.163   1190
  Planarity :  0.003   0.031   1260
  Dihedral  :  3.320  14.152    980
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.78 (0.28), residues: 910
  helix:  2.37 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.84 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  89 
 TYR   0.020   0.002   TYR E  61 
 PHE   0.004   0.001   PHE B 120 
 TRP   0.003   0.001   TRP E  47 
 HIS   0.001   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7485)
  covalent geometry    : angle       0.49235 (10080)
  hydrogen bonds       : bond        0.04242 (  455)
  hydrogen bonds       : angle       3.83641 ( 1350)

*********************** 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
  202 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8395 (t0) cc_final: 0.8148 (t0)
REVERT: A   48 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7763 (mtmm)
REVERT: A   60 GLU cc_start: 0.8696 (tt0) cc_final: 0.8396 (tt0)
REVERT: A  100 LYS cc_start: 0.8681 (mtmt) cc_final: 0.7724 (ttpt)
REVERT: A  164 GLU cc_start: 0.8523 (mp0) cc_final: 0.8221 (mp0)
REVERT: B   39 MET cc_start: 0.7827 (tpt) cc_final: 0.7477 (mmm)
REVERT: B   48 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8294 (mtmm)
REVERT: B   77 ARG cc_start: 0.8344 (ttt180) cc_final: 0.7833 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7186 (ttpp)
REVERT: B  111 MET cc_start: 0.8269 (ttm) cc_final: 0.7870 (ttp)
REVERT: C  100 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7532 (ttmm)
REVERT: C  122 GLU cc_start: 0.8528 (tt0) cc_final: 0.8253 (mt-10)
REVERT: C  159 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: C  177 ASP cc_start: 0.8014 (t0) cc_final: 0.7755 (t0)
REVERT: C  182 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7884 (mp)
REVERT: D   60 GLU cc_start: 0.8364 (tt0) cc_final: 0.8026 (tt0)
REVERT: D   87 TYR cc_start: 0.8996 (m-80) cc_final: 0.8588 (m-80)
REVERT: D  100 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7725 (tttp)
REVERT: D  101 ARG cc_start: 0.8634 (ttm170) cc_final: 0.8392 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7807 (mt-10)
REVERT: D  184 ASN cc_start: 0.8211 (t0) cc_final: 0.7896 (t0)
REVERT: E    6 ASN cc_start: 0.8480 (t0) cc_final: 0.8219 (t0)
REVERT: E   84 ASP cc_start: 0.8785 (m-30) cc_final: 0.8411 (m-30)
  outliers start: 21
  outliers final: 16
  residues processed: 197
  average time/residue: 0.1033
  time to fit residues: 26.3165
Evaluate side-chains
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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   44 ASP
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    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  186 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 6 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.130769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.108371 restraints weight = 8824.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.72
r_work: 0.2844 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2707

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= 0.116
  Angle     :  0.478   9.593  10080  Z= 0.260
  Chirality :  0.036   0.165   1190
  Planarity :  0.003   0.030   1260
  Dihedral  :  3.281  13.258    980
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.28), residues: 910
  helix:  2.49 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.90 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  89 
 TYR   0.021   0.002   TYR D  87 
 PHE   0.005   0.001   PHE B 120 
 TRP   0.004   0.001   TRP B  47 
 HIS   0.001   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7485)
  covalent geometry    : angle       0.47824 (10080)
  hydrogen bonds       : bond        0.03853 (  455)
  hydrogen bonds       : angle       3.80932 ( 1350)

*********************** 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: 18
    poor density    : 183
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8627 (t0) cc_final: 0.8383 (t0)
REVERT: A   48 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7716 (mtmm)
REVERT: A   60 GLU cc_start: 0.8731 (tt0) cc_final: 0.8371 (tt0)
REVERT: A  100 LYS cc_start: 0.8625 (mtmt) cc_final: 0.7645 (ttpt)
REVERT: A  164 GLU cc_start: 0.8597 (mp0) cc_final: 0.8288 (mp0)
REVERT: B   39 MET cc_start: 0.7838 (tpt) cc_final: 0.7416 (mmm)
REVERT: B   48 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8255 (mtmm)
REVERT: B   77 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7896 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7102 (ttpp)
REVERT: B  111 MET cc_start: 0.8144 (ttm) cc_final: 0.7723 (ttp)
REVERT: C  100 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7515 (ttmm)
REVERT: C  122 GLU cc_start: 0.8564 (tt0) cc_final: 0.8248 (mt-10)
REVERT: C  159 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8313 (mt-10)
REVERT: C  177 ASP cc_start: 0.7984 (t0) cc_final: 0.7707 (t0)
REVERT: D   49 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7505 (mmmt)
REVERT: D   60 GLU cc_start: 0.8388 (tt0) cc_final: 0.8016 (tt0)
REVERT: D  100 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7664 (tttp)
REVERT: D  101 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8349 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: E    6 ASN cc_start: 0.8454 (t0) cc_final: 0.8050 (t0)
REVERT: E   84 ASP cc_start: 0.8764 (m-30) cc_final: 0.8384 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 198
  average time/residue: 0.1074
  time to fit residues: 27.3816
Evaluate side-chains
  183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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   44 ASP
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  186 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3264 r_free = 0.3264 target = 0.120553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.096730 restraints weight = 9150.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.88
r_work: 0.2862 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2779

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= 0.149
  Angle     :  0.519   9.191  10080  Z= 0.279
  Chirality :  0.037   0.172   1190
  Planarity :  0.003   0.029   1260
  Dihedral  :  3.305  14.458    980
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.00 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.28), residues: 910
  helix:  2.39 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.84 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  89 
 TYR   0.031   0.003   TYR D  87 
 PHE   0.005   0.001   PHE B 120 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.001   0.000   HIS D 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7485)
  covalent geometry    : angle       0.51892 (10080)
  hydrogen bonds       : bond        0.04198 (  455)
  hydrogen bonds       : angle       3.83019 ( 1350)

********************** 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
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8570 (t0) cc_final: 0.8319 (t0)
REVERT: A   48 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7729 (mtmm)
REVERT: A   60 GLU cc_start: 0.8745 (tt0) cc_final: 0.8388 (tt0)
REVERT: A  100 LYS cc_start: 0.8639 (mtmt) cc_final: 0.7656 (ttpt)
REVERT: A  164 GLU cc_start: 0.8689 (mp0) cc_final: 0.8444 (mp0)
REVERT: B   39 MET cc_start: 0.7856 (tpt) cc_final: 0.7423 (mmm)
REVERT: B   48 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8276 (mtmm)
REVERT: B   77 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7918 (ttm-80)
REVERT: B  100 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7114 (ttpp)
REVERT: B  111 MET cc_start: 0.8279 (ttm) cc_final: 0.7850 (ttp)
REVERT: C  100 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7492 (ttmm)
REVERT: C  122 GLU cc_start: 0.8582 (tt0) cc_final: 0.8242 (mt-10)
REVERT: C  159 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8314 (mt-10)
REVERT: C  177 ASP cc_start: 0.8046 (t0) cc_final: 0.7790 (t0)
REVERT: C  182 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7864 (mp)
REVERT: D   60 GLU cc_start: 0.8413 (tt0) cc_final: 0.8061 (tt0)
REVERT: D   87 TYR cc_start: 0.8911 (m-80) cc_final: 0.8650 (m-80)
REVERT: D  100 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7653 (tttp)
REVERT: D  101 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8363 (ttm-80)
REVERT: D  159 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7857 (mt-10)
REVERT: E    6 ASN cc_start: 0.8577 (t0) cc_final: 0.8229 (t0)
REVERT: E   84 ASP cc_start: 0.8813 (m-30) cc_final: 0.8427 (m-30)
  outliers start: 20
  outliers final: 16
  residues processed: 184
  average time/residue: 0.1144
  time to fit residues: 26.9245
Evaluate side-chains
  176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   22 ILE
Chi-restraints excluded: chain C residue   44 ASP
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    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  186 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.121009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.096729 restraints weight = 9042.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.94
r_work: 0.2846 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7485  Z= 0.125
  Angle     :  0.503  10.388  10080  Z= 0.274
  Chirality :  0.037   0.169   1190
  Planarity :  0.003   0.028   1260
  Dihedral  :  3.310  14.129    980
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.88 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.28), residues: 910
  helix:  2.43 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.87 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  89 
 TYR   0.029   0.002   TYR D  87 
 PHE   0.005   0.001   PHE B 120 
 TRP   0.003   0.001   TRP B  47 
 HIS   0.001   0.000   HIS E 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7485)
  covalent geometry    : angle       0.50344 (10080)
  hydrogen bonds       : bond        0.04008 (  455)
  hydrogen bonds       : angle       3.84074 ( 1350)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2264.76 seconds
wall clock time: 39 minutes 36.88 seconds (2376.88 seconds total)