Starting phenix.real_space_refine
on Mon Feb 10 19:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xtb_10618/02_2025/6xtb_10618.cif"
  }
  resolution = 4.3
  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=   0.000 sd=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C     691      2.51       5
     N     235      2.21       5
     O     235      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 1161
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 1161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1161
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 212}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 750
          Unresolved non-hydrogen angles: 966
          Unresolved non-hydrogen dihedrals: 614
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 18, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 415
  Time building chain proxies: 1.48, per 1000 atoms: 1.27
  Number of scatterers: 1161
  At special positions: 0
  Unit cell: (57.78, 80.25, 70.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     235      8.00
     N     235      7.00
     C     691      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: 0.21
  Conformation dependent library (CDL) restraints added in 763.0 milliseconds
  

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  442

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 3 sheets defined
      11.9% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'E' and resid 119 through 134
      removed outlier: 3.534A  pdb=" N   MET E 125 " --> pdb=" O   PHE E 121 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ALA E 126 " --> pdb=" O   THR E 122 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   HIS E 128 " --> pdb=" O   VAL E 124 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR E 131 " --> pdb=" O   VAL E 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 242 through 253
      removed outlier: 3.982A  pdb=" N   LYS E 248 " --> pdb=" O   GLN E 244 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU E 249 " --> pdb=" O   GLU E 245 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 57 through 58
      removed outlier: 5.981A  pdb=" N   GLY E  48 " --> pdb=" O   SER E  36 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ASP E  32 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   PHE E 106 " --> pdb=" O   ILE E  97 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE E  97 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU E  95 " --> pdb=" O   PHE E 108 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   TYR E  96 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ILE E  79 " --> pdb=" O   TYR E  96 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   LEU E  98 " --> pdb=" O   LEU E  77 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 160 through 167
      removed outlier: 6.309A  pdb=" N   ILE E 182 " --> pdb=" O   TYR E 161 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   LYS E 163 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   PHE E 180 " --> pdb=" O   LYS E 163 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   ASN E 165 " --> pdb=" O   GLY E 178 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   GLY E 178 " --> pdb=" O   ASN E 165 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE E 181 " --> pdb=" O   VAL E 188 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL E 188 " --> pdb=" O   PHE E 181 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   THR E 183 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   ARG E 186 " --> pdb=" O   THR E 183 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL E 199 " --> pdb=" O   TRP E 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 206 through 212

    36 hydrogen bonds defined for protein.
    105 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: 0.22

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 235
        1.29 -     1.35: 232
        1.35 -     1.41: 1
        1.41 -     1.48: 234
        1.48 -     1.54: 457
  Bond restraints: 1159
  Sorted by residual:
  bond pdb=" C   ARG E  25 "
       pdb=" N   PRO E  26 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.17e-02 7.31e+03 5.11e+00
  bond pdb=" CA  VAL E 240 "
       pdb=" CB  VAL E 240 "
    ideal  model  delta    sigma   weight residual
    1.544  1.521  0.023 1.25e-02 6.40e+03 3.52e+00
  bond pdb=" CA  VAL E  13 "
       pdb=" CB  VAL E  13 "
    ideal  model  delta    sigma   weight residual
    1.544  1.521  0.023 1.25e-02 6.40e+03 3.42e+00
  bond pdb=" CA  VAL E  71 "
       pdb=" CB  VAL E  71 "
    ideal  model  delta    sigma   weight residual
    1.548  1.522  0.027 1.49e-02 4.50e+03 3.27e+00
  bond pdb=" CA  ILE E 211 "
       pdb=" CB  ILE E 211 "
    ideal  model  delta    sigma   weight residual
    1.541  1.521  0.021 1.27e-02 6.20e+03 2.61e+00
  ... (remaining 1154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 1417
        1.57 -     3.14: 159
        3.14 -     4.71: 23
        4.71 -     6.28: 6
        6.28 -     7.85: 6
  Bond angle restraints: 1611
  Sorted by residual:
  angle pdb=" N   PRO E 156 "
        pdb=" CA  PRO E 156 "
        pdb=" CB  PRO E 156 "
      ideal   model   delta    sigma   weight residual
     103.33  110.46   -7.13 9.30e-01 1.16e+00 5.87e+01
  angle pdb=" N   PRO E 115 "
        pdb=" CA  PRO E 115 "
        pdb=" CB  PRO E 115 "
      ideal   model   delta    sigma   weight residual
     101.88  109.35   -7.47 1.01e+00 9.80e-01 5.47e+01
  angle pdb=" N   PRO E 239 "
        pdb=" CA  PRO E 239 "
        pdb=" CB  PRO E 239 "
      ideal   model   delta    sigma   weight residual
     103.25  110.99   -7.74 1.05e+00 9.07e-01 5.44e+01
  angle pdb=" N   PRO E  26 "
        pdb=" CA  PRO E  26 "
        pdb=" CB  PRO E  26 "
      ideal   model   delta    sigma   weight residual
     103.36  109.66   -6.30 8.80e-01 1.29e+00 5.12e+01
  angle pdb=" N   PRO E 202 "
        pdb=" CA  PRO E 202 "
        pdb=" CB  PRO E 202 "
      ideal   model   delta    sigma   weight residual
     102.85  110.70   -7.85 1.13e+00 7.83e-01 4.82e+01
  ... (remaining 1606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.55: 550
        5.55 -    11.11: 83
       11.11 -    16.66: 33
       16.66 -    22.21: 3
       22.21 -    27.76: 6
  Dihedral angle restraints: 675
    sinusoidal: 0
      harmonic: 675
  Sorted by residual:
  dihedral pdb=" CA  ILE E  57 "
           pdb=" C   ILE E  57 "
           pdb=" N   LEU E  58 "
           pdb=" CA  LEU E  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.24  -27.76     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  TYR E  96 "
           pdb=" C   TYR E  96 "
           pdb=" N   ILE E  97 "
           pdb=" CA  ILE E  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.76  -27.24     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  LYS E  87 "
           pdb=" C   LYS E  87 "
           pdb=" N   LEU E  88 "
           pdb=" CA  LEU E  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.10   24.90     0      5.00e+00 4.00e-02 2.48e+01
  ... (remaining 672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 152
       0.059 -    0.119: 61
       0.119 -    0.178: 2
       0.178 -    0.237: 3
       0.237 -    0.296: 3
  Chirality restraints: 221
  Sorted by residual:
  chirality pdb=" CA  PRO E 115 "
            pdb=" N   PRO E 115 "
            pdb=" C   PRO E 115 "
            pdb=" CB  PRO E 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CA  PRO E 118 "
            pdb=" N   PRO E 118 "
            pdb=" C   PRO E 118 "
            pdb=" CB  PRO E 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  PRO E  26 "
            pdb=" N   PRO E  26 "
            pdb=" C   PRO E  26 "
            pdb=" CB  PRO E  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 218 not shown)

  Planarity restraints: 233
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  88 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.97e+00
        pdb=" C   LEU E  88 "    0.034 2.00e-02 2.50e+03
        pdb=" O   LEU E  88 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG E  89 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E  41 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" C   LYS E  41 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS E  41 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY E  42 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 217 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.99e+00
        pdb=" C   GLY E 217 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLY E 217 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU E 218 "    0.008 2.00e-02 2.50e+03
  ... (remaining 230 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 429
        2.88 -     3.38: 916
        3.38 -     3.89: 1490
        3.89 -     4.39: 1327
        4.39 -     4.90: 2446
  Nonbonded interactions: 6608
  Sorted by model distance:
  nonbonded pdb=" N   ARG E  49 "
            pdb=" O   HIS E  60 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" N   THR E  92 "
            pdb=" N   GLU E  93 "
     model   vdw
     2.524 2.560
  nonbonded pdb=" O   SER E  36 "
            pdb=" N   THR E 111 "
     model   vdw
     2.531 3.120
  nonbonded pdb=" N   THR E  83 "
            pdb=" O   THR E  83 "
     model   vdw
     2.599 2.496
  nonbonded pdb=" N   ILE E  37 "
            pdb=" O   GLY E  48 "
     model   vdw
     2.605 3.120
  ... (remaining 6603 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.840
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.030
  Process input model:                     7.950
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:2.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4468
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      :  0.006   0.027   1159  Z= 0.460
  Angle     :  1.171   7.847   1611  Z= 0.835
  Chirality :  0.066   0.296    221
  Planarity :  0.004   0.020    233
  Dihedral  :  8.676  27.764    233
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.58 %
    Favored  : 84.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.66 (0.42), residues: 231
  helix: -4.08 (0.49), residues: 32
  sheet: -3.25 (0.72), residues: 33
  loop : -3.08 (0.39), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.139 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0373
  time to fit residues: 0.3650
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0050
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 20 optimal weight:    7.9990
   chunk 14 optimal weight:   40.0000
   overall best weight:    5.2000

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.096019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.085527 restraints weight = 17133.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.085754 restraints weight = 16179.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.085839 restraints weight = 15496.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5375
moved from start:          0.5494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   1159  Z= 0.203
  Angle     :  0.618   4.520   1611  Z= 0.376
  Chirality :  0.049   0.135    221
  Planarity :  0.003   0.011    233
  Dihedral  :  6.051  15.474    233
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.84 (0.42), residues: 231
  helix: -3.96 (0.47), residues: 33
  sheet: -2.79 (0.66), residues: 56
  loop : -3.35 (0.38), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.110 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0130
  time to fit residues: 0.2357
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   chunk 1 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:   40.0000
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:   40.0000
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    3.8986

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.093611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.083469 restraints weight = 16424.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.083712 restraints weight = 14979.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.083971 restraints weight = 14019.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5496
moved from start:          0.7231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   1159  Z= 0.163
  Angle     :  0.526   3.640   1611  Z= 0.320
  Chirality :  0.048   0.128    221
  Planarity :  0.002   0.007    233
  Dihedral  :  5.073  15.447    233
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.45), residues: 231
  helix: -3.57 (0.53), residues: 33
  sheet: -2.48 (0.74), residues: 47
  loop : -3.13 (0.42), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.130 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0146
  time to fit residues: 0.2711
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 16 optimal weight:   40.0000
   chunk 8 optimal weight:    0.9990
   overall best weight:    4.3588

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.092593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.079668 restraints weight = 7976.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.080034 restraints weight = 7301.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.080090 restraints weight = 6837.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.9899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1159  Z= 0.180
  Angle     :  0.595   4.719   1611  Z= 0.355
  Chirality :  0.048   0.128    221
  Planarity :  0.003   0.007    233
  Dihedral  :  5.919  20.746    233
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.99 %
    Favored  : 87.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.51 (0.50), residues: 231
  helix: -3.25 (0.65), residues: 33
  sheet: -2.02 (0.75), residues: 55
  loop : -3.53 (0.45), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.139 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0149
  time to fit residues: 0.2773
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 14 optimal weight:   40.0000
   chunk 12 optimal weight:   20.0000
   chunk 18 optimal weight:    8.9990
   chunk 5 optimal weight:   30.0000
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0010
   chunk 1 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 13 optimal weight:    0.0570
   overall best weight:    4.4110

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.091193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.078540 restraints weight = 8247.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 15)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.078786 restraints weight = 7535.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.079102 restraints weight = 7115.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          1.0413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   1159  Z= 0.155
  Angle     :  0.537   4.883   1611  Z= 0.318
  Chirality :  0.047   0.129    221
  Planarity :  0.002   0.009    233
  Dihedral  :  5.357  19.872    233
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.15 %
    Favored  : 84.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.51 (0.51), residues: 231
  helix: -2.65 (0.76), residues: 33
  sheet: -2.61 (0.64), residues: 67
  loop : -3.40 (0.50), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.131 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0150
  time to fit residues: 0.2762
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0170
   chunk 8 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    5.1424

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.089521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.077303 restraints weight = 8065.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.077674 restraints weight = 7431.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.077674 restraints weight = 6881.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6171
moved from start:          1.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   1159  Z= 0.173
  Angle     :  0.575   4.482   1611  Z= 0.341
  Chirality :  0.048   0.128    221
  Planarity :  0.003   0.012    233
  Dihedral  :  5.790  22.346    233
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.58 %
    Favored  : 84.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (0.52), residues: 231
  helix: -2.38 (0.82), residues: 33
  sheet: -2.50 (0.65), residues: 66
  loop : -3.52 (0.50), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.147 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0221
  time to fit residues: 0.4103
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:   30.0000
   chunk 13 optimal weight:   20.0000
   chunk 5 optimal weight:   30.0000
   chunk 21 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.087566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.075357 restraints weight = 8353.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.075819 restraints weight = 7438.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.075821 restraints weight = 6777.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          1.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   1159  Z= 0.197
  Angle     :  0.634   5.602   1611  Z= 0.372
  Chirality :  0.048   0.129    221
  Planarity :  0.003   0.014    233
  Dihedral  :  6.474  25.704    233
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.91 %
    Favored  : 80.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.51), residues: 231
  helix: -2.47 (0.79), residues: 33
  sheet: -2.53 (0.69), residues: 52
  loop : -3.40 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.129 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0158
  time to fit residues: 0.2737
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 19 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:   30.0000
   chunk 15 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 16 optimal weight:   40.0000
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:   30.0000
   chunk 9 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:   10.7994

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.084201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.073135 restraints weight = 8608.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.073589 restraints weight = 7618.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.073765 restraints weight = 6950.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          1.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   1159  Z= 0.317
  Angle     :  0.847   6.411   1611  Z= 0.508
  Chirality :  0.050   0.128    221
  Planarity :  0.005   0.016    233
  Dihedral  :  8.315  24.963    233
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.65 %
    Favored  : 78.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.30 (0.46), residues: 231
  helix: -2.77 (0.75), residues: 31
  sheet: -3.50 (0.74), residues: 49
  loop : -3.94 (0.40), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.138 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0160
  time to fit residues: 0.2909
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 19 optimal weight:   30.0000
   chunk 6 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:   20.0000
   chunk 16 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 21 optimal weight:   50.0000
   chunk 18 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    4.2788

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.085563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.074093 restraints weight = 8357.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.074614 restraints weight = 7416.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.074800 restraints weight = 6762.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
moved from start:          1.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1159  Z= 0.147
  Angle     :  0.585   5.543   1611  Z= 0.348
  Chirality :  0.048   0.126    221
  Planarity :  0.002   0.010    233
  Dihedral  :  6.440  24.468    233
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.58 %
    Favored  : 84.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.90 (0.49), residues: 231
  helix: -2.43 (0.84), residues: 31
  sheet: -2.98 (0.75), residues: 51
  loop : -3.77 (0.42), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0136
  time to fit residues: 0.2584
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 4 optimal weight:   30.0000
   overall best weight:   11.5996

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.081905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.073691 restraints weight = 8846.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.074296 restraints weight = 7107.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.074746 restraints weight = 6077.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6370
moved from start:          1.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   1159  Z= 0.347
  Angle     :  0.930   8.247   1611  Z= 0.556
  Chirality :  0.051   0.127    221
  Planarity :  0.005   0.015    233
  Dihedral  :  9.155  28.884    233
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.71 %
    Favored  : 72.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.89 (0.45), residues: 231
  helix: -3.29 (0.73), residues: 31
  sheet: -3.46 (0.71), residues: 56
  loop : -4.51 (0.38), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 

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

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

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  462 Ramachandran restraints generated.
    231 Oldfield, 0 Emsley, 231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0157
  time to fit residues: 0.3300
Evaluate side-chains
  3 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 14 optimal weight:   30.0000
   overall best weight:   11.7992

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.081693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.070922 restraints weight = 8862.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.071461 restraints weight = 7607.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.071630 restraints weight = 6879.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          1.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   1159  Z= 0.341
  Angle     :  0.901   8.355   1611  Z= 0.543
  Chirality :  0.051   0.129    221
  Planarity :  0.005   0.019    233
  Dihedral  :  9.454  27.766    233
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.54 %
    Favored  : 74.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.23 (0.44), residues: 231
  helix: -3.76 (0.69), residues: 31
  sheet: -3.66 (0.68), residues: 58
  loop : -4.70 (0.37), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP E   8 
 PHE   0.000   0.000   PHE E  15 
 TYR   0.000   0.000   TYR E  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 704.92 seconds
wall clock time: 13 minutes 50.19 seconds (830.19 seconds total)