Starting phenix.real_space_refine
on Tue Feb 11 02:13:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kge_37218/02_2025/8kge_37218.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.084
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      10      5.16       5
     C    2238      2.51       5
     N     604      2.21       5
     O     732      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3584
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "V"
      Number of atoms: 1792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1792
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 11, 'TRANS': 231}
    Chain: "v"
      Number of atoms: 1792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1792
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 11, 'TRANS': 231}
  Time building chain proxies: 2.90, per 1000 atoms: 0.81
  Number of scatterers: 3584
  At special positions: 0
  Unit cell: (93.4554, 106.346, 82.7134, 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      10     16.00
     O     732      8.00
     N     604      7.00
     C    2238      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: 0.84
  Conformation dependent library (CDL) restraints added in 517.3 milliseconds
  

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 8 sheets defined
      6.2% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'V' and resid 92 through 103
    Processing helix  chain 'v' and resid 92 through 103
    Processing helix  chain 'v' and resid 151 through 156
      removed outlier: 3.511A  pdb=" N   SER v 156 " --> pdb=" O   GLU v 153 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'V' and resid 36 through 38
      removed outlier: 5.281A  pdb=" N   ALA V 107 " --> pdb=" O   TYR V  20 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS V 142 " --> pdb=" O   SER V 125 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ILE V 127 " --> pdb=" O   THR V 140 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   THR V 140 " --> pdb=" O   ILE V 127 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   LYS V 129 " --> pdb=" O   THR V 138 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   THR V 138 " --> pdb=" O   LYS V 129 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ALA V  85 " --> pdb=" O   VAL V  42 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL V  42 " --> pdb=" O   ALA V  85 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'V' and resid 36 through 38
      removed outlier: 5.281A  pdb=" N   ALA V 107 " --> pdb=" O   TYR V  20 " (cutoff:3.500A)
      removed outlier: 17.128A  pdb=" N   ARG V 121 " --> pdb=" O   ASP v  56 " (cutoff:3.500A)
      removed outlier: 14.175A  pdb=" N   ASP v  56 " --> pdb=" O   ARG V 121 " (cutoff:3.500A)
      removed outlier: 12.143A  pdb=" N   TRP V 123 " --> pdb=" O   SER v  54 " (cutoff:3.500A)
      removed outlier: 9.353A  pdb=" N   SER v  54 " --> pdb=" O   TRP V 123 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   SER V 125 " --> pdb=" O   ALA v  52 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLN v  74 " --> pdb=" O   GLU v  53 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   TYR v  55 " --> pdb=" O   GLN v  72 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   GLN v  72 " --> pdb=" O   TYR v  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'V' and resid 51 through 56
      removed outlier: 6.569A  pdb=" N   THR V  51 " --> pdb=" O   LYS V  75 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   LYS V  75 " --> pdb=" O   THR V  51 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   GLU V  53 " --> pdb=" O   GLY V  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'V' and resid 164 through 166
      removed outlier: 3.537A  pdb=" N   ILE V 214 " --> pdb=" O   LEU V 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'V' and resid 196 through 197
      removed outlier: 3.811A  pdb=" N   GLY V 222 " --> pdb=" O   VAL V 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'v' and resid 36 through 38
      removed outlier: 5.291A  pdb=" N   ALA v 107 " --> pdb=" O   TYR v  20 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   VAL v 124 " --> pdb=" O   THR v 144 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   THR v 144 " --> pdb=" O   VAL v 124 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR v 138 " --> pdb=" O   ALA v 130 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA v  85 " --> pdb=" O   VAL v  42 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   VAL v  42 " --> pdb=" O   ALA v  85 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'v' and resid 165 through 166
    Processing sheet with id=AA8, first strand: chain 'v' and resid 195 through 197

    128 hydrogen bonds defined for protein.
    342 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: 0.85

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1178
        1.34 -     1.46: 837
        1.46 -     1.58: 1619
        1.58 -     1.70: 0
        1.70 -     1.82: 20
  Bond restraints: 3654
  Sorted by residual:
  bond pdb=" CG  PRO V 168 "
       pdb=" CD  PRO V 168 "
    ideal  model  delta    sigma   weight residual
    1.503  1.404  0.099 3.40e-02 8.65e+02 8.54e+00
  bond pdb=" CB  GLU V 240 "
       pdb=" CG  GLU V 240 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" CB  GLU v 102 "
       pdb=" CG  GLU v 102 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" C   GLN V 186 "
       pdb=" N   PRO V 187 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.27e+00
  bond pdb=" CA  GLU V 188 "
       pdb=" CB  GLU V 188 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.69e-02 3.50e+03 1.17e+00
  ... (remaining 3649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 4866
        2.48 -     4.96: 96
        4.96 -     7.44: 18
        7.44 -     9.92: 4
        9.92 -    12.40: 4
  Bond angle restraints: 4988
  Sorted by residual:
  angle pdb=" N   PRO V 168 "
        pdb=" CD  PRO V 168 "
        pdb=" CG  PRO V 168 "
      ideal   model   delta    sigma   weight residual
     103.20   92.89   10.31 1.50e+00 4.44e-01 4.72e+01
  angle pdb=" CA  PRO V 168 "
        pdb=" N   PRO V 168 "
        pdb=" CD  PRO V 168 "
      ideal   model   delta    sigma   weight residual
     112.00  104.64    7.36 1.40e+00 5.10e-01 2.77e+01
  angle pdb=" CA  PRO V 168 "
        pdb=" CB  PRO V 168 "
        pdb=" CG  PRO V 168 "
      ideal   model   delta    sigma   weight residual
     104.50   96.47    8.03 1.90e+00 2.77e-01 1.79e+01
  angle pdb=" CB  MET V 151 "
        pdb=" CG  MET V 151 "
        pdb=" SD  MET V 151 "
      ideal   model   delta    sigma   weight residual
     112.70  125.10  -12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" CB  MET v 151 "
        pdb=" CG  MET v 151 "
        pdb=" SD  MET v 151 "
      ideal   model   delta    sigma   weight residual
     112.70  124.70  -12.00 3.00e+00 1.11e-01 1.60e+01
  ... (remaining 4983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.87: 1764
       14.87 -    29.73: 263
       29.73 -    44.60: 106
       44.60 -    59.46: 21
       59.46 -    74.33: 6
  Dihedral angle restraints: 2160
    sinusoidal: 786
      harmonic: 1374
  Sorted by residual:
  dihedral pdb=" CA  GLN v 186 "
           pdb=" C   GLN v 186 "
           pdb=" N   PRO v 187 "
           pdb=" CA  PRO v 187 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  GLY V 176 "
           pdb=" C   GLY V 176 "
           pdb=" N   GLN V 177 "
           pdb=" CA  GLN V 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.01  -16.99     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ASP V 192 "
           pdb=" C   ASP V 192 "
           pdb=" N   LYS V 193 "
           pdb=" CA  LYS V 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.17  -15.83     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 2157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 398
       0.037 -    0.074: 106
       0.074 -    0.111: 66
       0.111 -    0.148: 16
       0.148 -    0.185: 4
  Chirality restraints: 590
  Sorted by residual:
  chirality pdb=" CA  ILE V 241 "
            pdb=" N   ILE V 241 "
            pdb=" C   ILE V 241 "
            pdb=" CB  ILE V 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CB  THR V 162 "
            pdb=" CA  THR V 162 "
            pdb=" OG1 THR V 162 "
            pdb=" CG2 THR V 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  GLU V 188 "
            pdb=" N   GLU V 188 "
            pdb=" C   GLU V 188 "
            pdb=" CB  GLU V 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 587 not shown)

  Planarity restraints: 640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN V 186 "    0.047 5.00e-02 4.00e+02   7.28e-02 8.49e+00
        pdb=" N   PRO V 187 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO V 187 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO V 187 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE v 226 "   -0.039 5.00e-02 4.00e+02   5.95e-02 5.66e+00
        pdb=" N   PRO v 227 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO v 227 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO v 227 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE v 226 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.84e+00
        pdb=" C   ILE v 226 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ILE v 226 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO v 227 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 637 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 104
        2.66 -     3.22: 3308
        3.22 -     3.78: 5243
        3.78 -     4.34: 6751
        4.34 -     4.90: 11634
  Nonbonded interactions: 27040
  Sorted by model distance:
  nonbonded pdb=" OG1 THR V 180 "
            pdb=" OG1 THR V 213 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" OH  TYR V 108 "
            pdb=" OD1 ASN V 145 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" NE2 GLN V 177 "
            pdb=" O   VAL V 216 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OG1 THR v 206 "
            pdb=" OD1 ASN v 217 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NZ  LYS V 129 "
            pdb=" OD2 ASP v 118 "
     model   vdw
     2.299 3.120
  ... (remaining 27035 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 'V'
  selection = chain 'v'
}

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 group one per residue
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:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.190
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
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      :  0.004   0.099   3654  Z= 0.266
  Angle     :  0.871  12.404   4988  Z= 0.444
  Chirality :  0.048   0.185    590
  Planarity :  0.005   0.073    640
  Dihedral  : 17.206  74.325   1280
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.34 %
    Favored  : 90.46 %
  Rotamer:
    Outliers : 10.88 %
    Allowed  : 34.72 %
    Favored  : 54.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.35), residues: 482
  helix:  1.37 (1.06), residues: 24
  sheet: -0.83 (0.34), residues: 222
  loop : -2.53 (0.33), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP V 123 
 PHE   0.014   0.002   PHE V 120 
 TYR   0.005   0.001   TYR V  55 
 ARG   0.004   0.000   ARG V 139 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 50
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 37
  residues processed: 89
  average time/residue: 0.1233
  time to fit residues: 14.0856
Evaluate side-chains
  84 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 47
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  132 THR
Chi-restraints excluded: chain V residue  141 VAL
Chi-restraints excluded: chain V residue  157 THR
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  204 LYS
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   33 ASP
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   79 ASP
Chi-restraints excluded: chain v residue   80 THR
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  105 THR
Chi-restraints excluded: chain v residue  110 ILE
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  125 SER
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  138 THR
Chi-restraints excluded: chain v residue  156 SER
Chi-restraints excluded: chain v residue  157 THR
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  219 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
V  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.117454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.101411 restraints weight = 8612.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103167 restraints weight = 4404.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104253 restraints weight = 2742.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3654  Z= 0.181
  Angle     :  0.655   7.553   4988  Z= 0.326
  Chirality :  0.047   0.149    590
  Planarity :  0.005   0.057    640
  Dihedral  :  8.825  69.198    567
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.92 %
    Favored  : 90.87 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 29.02 %
    Favored  : 60.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.35), residues: 482
  helix:  2.15 (0.98), residues: 24
  sheet: -0.68 (0.34), residues: 221
  loop : -2.40 (0.33), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP v  18 
 PHE   0.012   0.002   PHE V 120 
 TYR   0.007   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 52
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7554 (tt0)
REVERT: V  111 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8276 (mmm-85)
REVERT: V  155 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5599 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7189 (p0)
  outliers start: 39
  outliers final: 27
  residues processed: 84
  average time/residue: 0.1816
  time to fit residues: 18.6965
Evaluate side-chains
  79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 48
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain V residue  242 THR
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  157 THR
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  177 GLN
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    2.9984

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

Flipped N/Q/H residues before XYZ refinement:
v  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.112471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.096578 restraints weight = 8647.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.098413 restraints weight = 4254.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.099572 restraints weight = 2574.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3654  Z= 0.294
  Angle     :  0.656   7.027   4988  Z= 0.330
  Chirality :  0.048   0.152    590
  Planarity :  0.005   0.052    640
  Dihedral  :  8.424  67.553    543
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers : 12.18 %
    Allowed  : 27.72 %
    Favored  : 60.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.35), residues: 482
  helix:  1.37 (0.98), residues: 25
  sheet: -0.90 (0.34), residues: 217
  loop : -2.51 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP v  18 
 PHE   0.015   0.002   PHE V 120 
 TYR   0.013   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 51
  time to evaluate  : 0.377 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: V  111 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8436 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.5933 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7229 (p0)
REVERT: v   87 MET cc_start: 0.4264 (mmt) cc_final: 0.3764 (mmt)
REVERT: v  177 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6216 (tp40)
  outliers start: 47
  outliers final: 33
  residues processed: 93
  average time/residue: 0.1567
  time to fit residues: 17.7382
Evaluate side-chains
  85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 47
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  214 ILE
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  105 THR
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  177 GLN
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.099162 restraints weight = 8655.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100958 restraints weight = 4290.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.102089 restraints weight = 2599.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3654  Z= 0.195
  Angle     :  0.628   7.188   4988  Z= 0.314
  Chirality :  0.047   0.151    590
  Planarity :  0.004   0.052    640
  Dihedral  :  8.072  66.881    542
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 30.57 %
    Favored  : 59.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.35), residues: 482
  helix:  1.59 (1.00), residues: 25
  sheet: -0.88 (0.34), residues: 217
  loop : -2.49 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP v  18 
 PHE   0.017   0.002   PHE V 120 
 TYR   0.008   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 51
  time to evaluate  : 0.394 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7683 (tt0)
REVERT: V  111 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8339 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5827 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7136 (p0)
REVERT: v   72 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7958 (tt0)
REVERT: v  215 THR cc_start: 0.7709 (m) cc_final: 0.7487 (m)
  outliers start: 39
  outliers final: 30
  residues processed: 85
  average time/residue: 0.1557
  time to fit residues: 16.2042
Evaluate side-chains
  82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 47
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   17 LEU
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  181 LEU
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
v 145 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.116480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100590 restraints weight = 8741.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.102430 restraints weight = 4321.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.103500 restraints weight = 2614.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3654  Z= 0.168
  Angle     :  0.602   7.217   4988  Z= 0.298
  Chirality :  0.046   0.142    590
  Planarity :  0.004   0.052    640
  Dihedral  :  7.690  64.143    539
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers : 11.92 %
    Allowed  : 29.27 %
    Favored  : 58.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.35), residues: 482
  helix:  2.34 (1.02), residues: 24
  sheet: -0.96 (0.34), residues: 217
  loop : -2.35 (0.33), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP v  18 
 PHE   0.015   0.002   PHE V 120 
 TYR   0.006   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 52
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7527 (tt0)
REVERT: V  111 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8260 (mmm-85)
REVERT: V  155 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.5639 (mtt-85)
REVERT: V  206 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7394 (p)
REVERT: V  217 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7307 (p0)
REVERT: v   63 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: v   72 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7876 (tt0)
REVERT: v  215 THR cc_start: 0.7714 (m) cc_final: 0.7508 (m)
  outliers start: 46
  outliers final: 33
  residues processed: 90
  average time/residue: 0.1504
  time to fit residues: 16.7747
Evaluate side-chains
  89 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 49
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   17 LEU
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  110 ILE
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  181 LEU
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** v  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.110342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.094893 restraints weight = 8975.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.096683 restraints weight = 4408.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.097812 restraints weight = 2661.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3654  Z= 0.427
  Angle     :  0.735   7.194   4988  Z= 0.375
  Chirality :  0.051   0.177    590
  Planarity :  0.005   0.056    640
  Dihedral  :  8.589  63.378    539
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers : 11.66 %
    Allowed  : 29.79 %
    Favored  : 58.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.35), residues: 482
  helix:  1.14 (1.01), residues: 25
  sheet: -0.91 (0.35), residues: 213
  loop : -2.51 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP v 123 
 PHE   0.023   0.003   PHE V 120 
 TYR   0.017   0.002   TYR v  55 
 ARG   0.003   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 49
  time to evaluate  : 0.438 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7852 (tt0)
REVERT: V  111 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8483 (mmm-85)
REVERT: V  217 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7476 (p0)
REVERT: v   63 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6905 (mp0)
REVERT: v   72 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8073 (tt0)
REVERT: v   87 MET cc_start: 0.4451 (mmt) cc_final: 0.3927 (mmt)
  outliers start: 45
  outliers final: 35
  residues processed: 87
  average time/residue: 0.1390
  time to fit residues: 15.2357
Evaluate side-chains
  85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 45
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  214 ILE
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  105 THR
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  167 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  181 LEU
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
v  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.096629 restraints weight = 8739.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.098453 restraints weight = 4312.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.099588 restraints weight = 2605.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3654  Z= 0.291
  Angle     :  0.681   8.107   4988  Z= 0.344
  Chirality :  0.049   0.175    590
  Planarity :  0.004   0.055    640
  Dihedral  :  8.273  62.778    539
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers : 11.14 %
    Allowed  : 30.83 %
    Favored  : 58.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.35), residues: 482
  helix:  1.18 (1.01), residues: 25
  sheet: -1.04 (0.34), residues: 215
  loop : -2.51 (0.34), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP v 123 
 PHE   0.020   0.002   PHE V 120 
 TYR   0.013   0.002   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 49
  time to evaluate  : 0.407 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7798 (tt0)
REVERT: V  111 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8402 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6096 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7153 (p0)
REVERT: v   63 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6866 (mp0)
REVERT: v   87 MET cc_start: 0.4396 (mmt) cc_final: 0.3808 (mmt)
  outliers start: 43
  outliers final: 36
  residues processed: 85
  average time/residue: 0.1520
  time to fit residues: 15.8755
Evaluate side-chains
  90 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 49
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  213 THR
Chi-restraints excluded: chain V residue  214 ILE
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  158 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  167 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  181 LEU
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  193 LYS
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Chi-restraints excluded: chain v residue  241 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0270
   chunk 7 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0040
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.1454

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.115360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.099735 restraints weight = 8666.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.101584 restraints weight = 4273.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102631 restraints weight = 2580.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3654  Z= 0.176
  Angle     :  0.653   9.807   4988  Z= 0.325
  Chirality :  0.047   0.164    590
  Planarity :  0.004   0.055    640
  Dihedral  :  7.917  59.831    539
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers : 11.14 %
    Allowed  : 31.09 %
    Favored  : 57.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.35), residues: 482
  helix:  1.90 (1.01), residues: 24
  sheet: -0.73 (0.35), residues: 203
  loop : -2.39 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP v 123 
 PHE   0.017   0.002   PHE V 120 
 TYR   0.006   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 51
  time to evaluate  : 0.411 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (tt0)
REVERT: V  111 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8267 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5825 (mtt-85)
REVERT: V  181 LEU cc_start: 0.7496 (mm) cc_final: 0.7154 (tp)
REVERT: V  217 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7167 (p0)
REVERT: v   63 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6807 (mp0)
REVERT: v   72 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7887 (tt0)
  outliers start: 43
  outliers final: 33
  residues processed: 86
  average time/residue: 0.1562
  time to fit residues: 16.5262
Evaluate side-chains
  86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 47
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  119 VAL
Chi-restraints excluded: chain V residue  121 ARG
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  177 GLN
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   96 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  110 ILE
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  181 LEU
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  196 ARG
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Chi-restraints excluded: chain v residue  241 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0470
   chunk 41 optimal weight:    6.9990
   chunk 12 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.7080

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.117971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.102351 restraints weight = 8544.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.104117 restraints weight = 4310.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105285 restraints weight = 2633.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3654  Z= 0.155
  Angle     :  0.630  10.309   4988  Z= 0.308
  Chirality :  0.047   0.157    590
  Planarity :  0.004   0.054    640
  Dihedral  :  7.084  54.171    535
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.09 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  9.59 %
    Allowed  : 32.38 %
    Favored  : 58.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.35), residues: 482
  helix:  2.49 (1.02), residues: 24
  sheet: -0.56 (0.36), residues: 198
  loop : -2.32 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP v 123 
 PHE   0.014   0.002   PHE V 120 
 TYR   0.005   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 139 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 54
  time to evaluate  : 0.422 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7444 (tt0)
REVERT: V  111 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8222 (mmm-85)
REVERT: V  155 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.5563 (mtt-85)
REVERT: V  181 LEU cc_start: 0.7254 (mm) cc_final: 0.6975 (tp)
REVERT: V  206 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7436 (p)
REVERT: V  217 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7349 (p0)
REVERT: v   63 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6883 (mp0)
REVERT: v   72 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7662 (tt0)
  outliers start: 37
  outliers final: 26
  residues processed: 84
  average time/residue: 0.1481
  time to fit residues: 15.5797
Evaluate side-chains
  83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 50
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  206 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain V residue  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   84 LEU
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  110 ILE
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Chi-restraints excluded: chain v residue  241 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 42 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.118746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.102899 restraints weight = 8458.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104761 restraints weight = 4144.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105955 restraints weight = 2491.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3654  Z= 0.158
  Angle     :  0.640  11.161   4988  Z= 0.310
  Chirality :  0.046   0.145    590
  Planarity :  0.004   0.054    640
  Dihedral  :  6.320  51.618    532
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.68 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 33.68 %
    Favored  : 57.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.36), residues: 482
  helix:  2.58 (1.00), residues: 24
  sheet: -0.49 (0.36), residues: 202
  loop : -2.20 (0.33), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP v 123 
 PHE   0.015   0.002   PHE V 120 
 TYR   0.005   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 139 

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 53
  time to evaluate  : 0.399 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7440 (tt0)
REVERT: V  111 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7664 (mtm180)
REVERT: V  155 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.5503 (mtt-85)
REVERT: V  181 LEU cc_start: 0.7319 (mm) cc_final: 0.7035 (tp)
REVERT: V  217 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7032 (p0)
REVERT: v   63 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6888 (mp0)
REVERT: v   72 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7908 (tt0)
  outliers start: 33
  outliers final: 22
  residues processed: 79
  average time/residue: 0.1652
  time to fit residues: 16.0503
Evaluate side-chains
  79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 51
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   45 LEU
Chi-restraints excluded: chain V residue   46 THR
Chi-restraints excluded: chain V residue   83 THR
Chi-restraints excluded: chain V residue   90 GLU
Chi-restraints excluded: chain V residue  111 ARG
Chi-restraints excluded: chain V residue  117 VAL
Chi-restraints excluded: chain V residue  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  193 LYS
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  215 THR
Chi-restraints excluded: chain V residue  217 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   51 THR
Chi-restraints excluded: chain v residue   63 GLU
Chi-restraints excluded: chain v residue   72 GLN
Chi-restraints excluded: chain v residue   83 THR
Chi-restraints excluded: chain v residue   97 LEU
Chi-restraints excluded: chain v residue  110 ILE
Chi-restraints excluded: chain v residue  119 VAL
Chi-restraints excluded: chain v residue  131 VAL
Chi-restraints excluded: chain v residue  162 THR
Chi-restraints excluded: chain v residue  180 THR
Chi-restraints excluded: chain v residue  183 VAL
Chi-restraints excluded: chain v residue  201 ASP
Chi-restraints excluded: chain v residue  216 VAL
Chi-restraints excluded: chain v residue  228 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.118330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.102325 restraints weight = 8424.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.104214 restraints weight = 4055.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.105424 restraints weight = 2429.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3654  Z= 0.180
  Angle     :  0.648  11.013   4988  Z= 0.318
  Chirality :  0.047   0.147    590
  Planarity :  0.004   0.055    640
  Dihedral  :  6.083  51.423    528
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.51 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 33.68 %
    Favored  : 59.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.36), residues: 482
  helix:  2.68 (1.02), residues: 24
  sheet: -0.40 (0.37), residues: 203
  loop : -2.16 (0.33), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP v 123 
 PHE   0.017   0.002   PHE V 120 
 TYR   0.006   0.001   TYR v  55 
 ARG   0.002   0.000   ARG v 196 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1456.76 seconds
wall clock time: 26 minutes 45.49 seconds (1605.49 seconds total)