Starting phenix.real_space_refine
on Wed Mar  5 21:19:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kge_37218/03_2025/8kge_37218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kge_37218/03_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_37218/03_2025/8kge_37218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kge_37218/03_2025/8kge_37218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kge_37218/03_2025/8kge_37218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kge_37218/03_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-5624/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: 2.62, per 1000 atoms: 0.73
  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: 0.78
  Conformation dependent library (CDL) restraints added in 411.3 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: 0.47
  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: 0.97

  Time building geometry restraints manager: 0.92 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:             0.690
  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:                    0.030
  Process input model:                     12.720
  Find NCS groups from input model:        0.120
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
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  : 0.390 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 37
  residues processed: 89
  average time/residue: 0.1329
  time to fit residues: 15.2552
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  : 0.409 
-------------------------------------------------------------------------------
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  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 = 0.101412 restraints weight = 8612.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103167 restraints weight = 4404.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104254 restraints weight = 2742.496|
|-----------------------------------------------------------------------------|
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  : 0.403 
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: 0.1645
  time to fit residues: 16.8136
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  : 0.342 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0970
   chunk 24 optimal weight:    0.0980
   chunk 3 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0030
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.120232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.103963 restraints weight = 8532.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105837 restraints weight = 4261.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.107027 restraints weight = 2602.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3654  Z= 0.149
  Angle     :  0.593   7.348   4988  Z= 0.292
  Chirality :  0.046   0.141    590
  Planarity :  0.004   0.047    640
  Dihedral  :  7.841  67.191    543
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  9.59 %
    Allowed  : 29.53 %
    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: -1.93 (0.35), residues: 482
  helix:  2.59 (0.98), residues: 24
  sheet: -0.58 (0.36), residues: 203
  loop : -2.33 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP v  18 
 PHE   0.009   0.001   PHE v 235 
 TYR   0.005   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 139 

*********************** 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
  96 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 59
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7376 (tt0)
REVERT: V  111 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8153 (mmm-85)
REVERT: V  155 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.5633 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7276 (p0)
REVERT: v  215 THR cc_start: 0.7867 (m) cc_final: 0.7633 (m)
  outliers start: 37
  outliers final: 28
  residues processed: 88
  average time/residue: 0.1520
  time to fit residues: 16.4366
Evaluate side-chains
  84 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 52
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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  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  207 VAL
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   79 ASP
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  158 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  193 LYS
Chi-restraints excluded: chain v residue  195 PHE
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:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0050
   chunk 10 optimal weight:    6.9990
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.2796

-------------------------------------------------------------------------------
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 = 0.117947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.102037 restraints weight = 8661.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.103806 restraints weight = 4423.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104945 restraints weight = 2756.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1426

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= 0.173
  Angle     :  0.599   7.827   4988  Z= 0.294
  Chirality :  0.046   0.141    590
  Planarity :  0.004   0.045    640
  Dihedral  :  7.675  64.420    539
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  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: -1.88 (0.36), residues: 482
  helix:  2.61 (1.00), residues: 24
  sheet: -0.64 (0.35), residues: 213
  loop : -2.26 (0.33), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP v  18 
 PHE   0.022   0.002   PHE V  82 
 TYR   0.007   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
  91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 52
  time to evaluate  : 0.358 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7559 (tt0)
REVERT: V  111 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7641 (mtm180)
REVERT: V  155 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.5655 (mtt-85)
REVERT: V  177 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7302 (mp10)
REVERT: V  217 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7285 (p0)
REVERT: v   51 THR cc_start: 0.9088 (p) cc_final: 0.8846 (p)
REVERT: v  215 THR cc_start: 0.7869 (m) cc_final: 0.7630 (m)
  outliers start: 39
  outliers final: 26
  residues processed: 85
  average time/residue: 0.1457
  time to fit residues: 15.3121
Evaluate side-chains
  81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 50
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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  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   17 LEU
Chi-restraints excluded: chain v residue   70 THR
Chi-restraints excluded: chain v residue   84 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  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:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.117053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.101322 restraints weight = 8701.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.103149 restraints weight = 4242.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.104346 restraints weight = 2555.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3654  Z= 0.187
  Angle     :  0.614   7.661   4988  Z= 0.302
  Chirality :  0.047   0.143    590
  Planarity :  0.004   0.051    640
  Dihedral  :  7.733  62.370    539
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers : 10.36 %
    Allowed  : 30.05 %
    Favored  : 59.59 %
  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: -1.84 (0.36), residues: 482
  helix:  2.53 (0.99), residues: 24
  sheet: -0.61 (0.35), residues: 212
  loop : -2.22 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP v  18 
 PHE   0.019   0.002   PHE V  82 
 TYR   0.008   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
  91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 51
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: V  111 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7658 (mtm180)
REVERT: V  155 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5676 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7284 (p0)
REVERT: v   51 THR cc_start: 0.9087 (p) cc_final: 0.8831 (p)
REVERT: v   72 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7919 (tt0)
REVERT: v  215 THR cc_start: 0.7766 (m) cc_final: 0.7541 (m)
  outliers start: 40
  outliers final: 29
  residues processed: 86
  average time/residue: 0.1520
  time to fit residues: 16.0867
Evaluate side-chains
  83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 49
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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   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  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  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:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 3 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    4.0786

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.110971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.095584 restraints weight = 8924.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.097352 restraints weight = 4397.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.098456 restraints weight = 2666.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3654  Z= 0.374
  Angle     :  0.709   7.303   4988  Z= 0.358
  Chirality :  0.050   0.179    590
  Planarity :  0.005   0.054    640
  Dihedral  :  8.181  62.570    537
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers : 11.92 %
    Allowed  : 28.50 %
    Favored  : 59.59 %
  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: -2.22 (0.35), residues: 482
  helix:  1.36 (1.01), residues: 25
  sheet: -0.89 (0.34), residues: 218
  loop : -2.38 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP v 123 
 PHE   0.021   0.003   PHE V 120 
 TYR   0.015   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
  97 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 51
  time to evaluate  : 0.363 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7856 (tt0)
REVERT: V  111 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8432 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5890 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7372 (p0)
REVERT: v   51 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.9003 (p)
REVERT: v   63 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6817 (mp0)
REVERT: v   87 MET cc_start: 0.4396 (mmt) cc_final: 0.3885 (mmt)
  outliers start: 46
  outliers final: 35
  residues processed: 90
  average time/residue: 0.1525
  time to fit residues: 17.0072
Evaluate side-chains
  89 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 48
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  178 SER
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   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  117 VAL
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:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0060
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.4002

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.112809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.097336 restraints weight = 8770.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.099111 restraints weight = 4336.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.100258 restraints weight = 2639.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3654  Z= 0.245
  Angle     :  0.662   9.075   4988  Z= 0.330
  Chirality :  0.048   0.169    590
  Planarity :  0.004   0.053    640
  Dihedral  :  7.983  60.536    537
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers : 10.88 %
    Allowed  : 30.05 %
    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: -2.14 (0.35), residues: 482
  helix:  1.48 (1.01), residues: 25
  sheet: -0.78 (0.35), residues: 207
  loop : -2.35 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP v 123 
 PHE   0.019   0.002   PHE V 120 
 TYR   0.009   0.001   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: 42
    poor density    : 50
  time to evaluate  : 0.365 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7782 (tt0)
REVERT: V  111 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8315 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.5855 (mtt-85)
REVERT: V  217 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7425 (p0)
REVERT: v   51 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8926 (p)
REVERT: v   72 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8141 (tt0)
REVERT: v   87 MET cc_start: 0.4289 (mmt) cc_final: 0.3700 (mmt)
REVERT: v  196 ARG cc_start: 0.8198 (ppp80) cc_final: 0.7613 (ppp80)
REVERT: v  215 THR cc_start: 0.7791 (m) cc_final: 0.7579 (m)
  outliers start: 42
  outliers final: 34
  residues processed: 85
  average time/residue: 0.1439
  time to fit residues: 15.1288
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  : 0.362 
-------------------------------------------------------------------------------
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  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   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  110 ILE
Chi-restraints excluded: chain v residue  117 VAL
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:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0770
   chunk 4 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0170
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.116849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.101030 restraints weight = 8511.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102881 restraints weight = 4118.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.104051 restraints weight = 2465.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1961

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= 0.162
  Angle     :  0.641  10.531   4988  Z= 0.314
  Chirality :  0.047   0.157    590
  Planarity :  0.004   0.052    640
  Dihedral  :  7.005  59.807    534
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.47 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  8.81 %
    Allowed  : 31.87 %
    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: -1.86 (0.36), residues: 482
  helix:  2.32 (1.01), residues: 24
  sheet: -0.57 (0.35), residues: 208
  loop : -2.24 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP v  18 
 PHE   0.016   0.002   PHE V 120 
 TYR   0.006   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 139 

*********************** 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
  88 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 54
  time to evaluate  : 0.373 
Fit side-chains
REVERT: V   90 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: V  111 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8222 (mmm-85)
REVERT: V  155 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5597 (mtt-85)
REVERT: V  181 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7211 (tp)
REVERT: v   51 THR cc_start: 0.9089 (p) cc_final: 0.8830 (p)
REVERT: v  164 MET cc_start: 0.8272 (tmm) cc_final: 0.8032 (ptm)
REVERT: v  196 ARG cc_start: 0.8096 (ppp80) cc_final: 0.7568 (ppp80)
  outliers start: 34
  outliers final: 27
  residues processed: 83
  average time/residue: 0.1350
  time to fit residues: 14.1144
Evaluate side-chains
  80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 49
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
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  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  173 VAL
Chi-restraints excluded: chain V residue  181 LEU
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  232 ASN
Chi-restraints excluded: chain v residue   17 LEU
Chi-restraints excluded: chain v residue   70 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.113333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.097784 restraints weight = 8710.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.099591 restraints weight = 4281.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.100731 restraints weight = 2595.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3654  Z= 0.284
  Angle     :  0.689  10.780   4988  Z= 0.342
  Chirality :  0.048   0.161    590
  Planarity :  0.004   0.054    640
  Dihedral  :  7.297  54.866    534
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  9.33 %
    Allowed  : 32.64 %
    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: -1.88 (0.36), residues: 482
  helix:  1.94 (1.02), residues: 24
  sheet: -0.51 (0.36), residues: 203
  loop : -2.26 (0.33), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP v 123 
 PHE   0.027   0.003   PHE V 195 
 TYR   0.011   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

*********************** 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
  84 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 48
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7777 (tt0)
REVERT: V  111 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8326 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.5788 (mtt-85)
REVERT: V  181 LEU cc_start: 0.7477 (mm) cc_final: 0.7249 (tp)
REVERT: v   51 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8949 (p)
REVERT: v   63 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6849 (mp0)
REVERT: v   87 MET cc_start: 0.4116 (mmt) cc_final: 0.3578 (mmt)
REVERT: v  196 ARG cc_start: 0.8272 (ppp80) cc_final: 0.7691 (ppp80)
  outliers start: 36
  outliers final: 29
  residues processed: 80
  average time/residue: 0.1465
  time to fit residues: 14.6197
Evaluate side-chains
  82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 48
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  173 VAL
Chi-restraints excluded: chain V residue  178 SER
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  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   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  162 THR
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
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:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.115716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.100335 restraints weight = 8595.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.102075 restraints weight = 4354.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103162 restraints weight = 2682.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3654  Z= 0.188
  Angle     :  0.663  11.209   4988  Z= 0.325
  Chirality :  0.047   0.142    590
  Planarity :  0.004   0.053    640
  Dihedral  :  7.144  59.745    534
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  8.29 %
    Allowed  : 33.68 %
    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: -1.85 (0.36), residues: 482
  helix:  2.24 (1.02), residues: 24
  sheet: -0.49 (0.36), residues: 204
  loop : -2.27 (0.33), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP v 123 
 PHE   0.036   0.003   PHE V 195 
 TYR   0.007   0.001   TYR v  55 
 ARG   0.002   0.000   ARG V 155 

********************** 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
  83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: V   90 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (tt0)
REVERT: V  111 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8265 (mmm-85)
REVERT: V  155 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5646 (mtt-85)
REVERT: v   51 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8837 (p)
REVERT: v  196 ARG cc_start: 0.8100 (ppp80) cc_final: 0.7610 (ppp80)
  outliers start: 32
  outliers final: 26
  residues processed: 78
  average time/residue: 0.1496
  time to fit residues: 14.5049
Evaluate side-chains
  80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 50
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
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  127 ILE
Chi-restraints excluded: chain V residue  131 VAL
Chi-restraints excluded: chain V residue  155 ARG
Chi-restraints excluded: chain V residue  173 VAL
Chi-restraints excluded: chain V residue  203 THR
Chi-restraints excluded: chain V residue  215 THR
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   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  162 THR
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
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 4 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.111288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.095975 restraints weight = 8708.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.097742 restraints weight = 4339.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.098877 restraints weight = 2643.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3654  Z= 0.361
  Angle     :  0.739  10.888   4988  Z= 0.369
  Chirality :  0.049   0.151    590
  Planarity :  0.004   0.056    640
  Dihedral  :  7.481  53.979    530
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  9.84 %
    Allowed  : 31.35 %
    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: -2.06 (0.35), residues: 482
  helix:  1.58 (1.01), residues: 24
  sheet: -0.70 (0.35), residues: 204
  loop : -2.30 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP v 123 
 PHE   0.036   0.003   PHE V 195 
 TYR   0.013   0.002   TYR v  55 
 ARG   0.003   0.000   ARG V 155 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1451.39 seconds
wall clock time: 26 minutes 4.86 seconds (1564.86 seconds total)