Starting phenix.real_space_refine
on Fri Aug 22 12:37:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xtb_10618/08_2025/6xtb_10618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xtb_10618/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xtb_10618/08_2025/6xtb_10618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xtb_10618/08_2025/6xtb_10618.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xtb_10618/08_2025/6xtb_10618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xtb_10618/08_2025/6xtb_10618.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 13, 'TRP:plan': 4, 'GLU:plan': 11, 'ARG:plan': 16, 'PHE:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 6}
          Unresolved non-hydrogen planarities: 415
  Time building chain proxies: 0.52, per 1000 atoms: 0.45
  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: 0.06
  Conformation dependent library (CDL) restraints added in 59.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.04
  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: 0.07

  Time building geometry restraints manager: 0.08 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:             1.200
  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:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.520
  Find NCS groups from input model:        0.000
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.810
-------------------------------------------------------------------------------
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= 0.433
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 TYR   0.000   0.000   TYR E  73 
 PHE   0.000   0.000   PHE E  15 
 TRP   0.000   0.000   TRP E   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 1159)
  covalent geometry    : angle       1.17070 ( 1611)
  hydrogen bonds       : bond        0.31305 (   36)
  hydrogen bonds       : angle      11.92711 (  105)

*********************** 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  : 0.024 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0085
  time to fit residues: 0.0736
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  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    0.5980
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   overall best weight:    5.3188

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.096288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085144 restraints weight = 15206.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085144 restraints weight = 14675.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085144 restraints weight = 14675.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085144 restraints weight = 14675.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085144 restraints weight = 14675.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5398
moved from start:          0.5409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1159  Z= 0.209
  Angle     :  0.622   4.471   1611  Z= 0.382
  Chirality :  0.048   0.138    221
  Planarity :  0.003   0.010    233
  Dihedral  :  6.040  15.462    233
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.00
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.86 (0.43), residues: 231
  helix: -3.92 (0.48), residues: 33
  sheet: -2.92 (0.65), residues: 58
  loop : -3.31 (0.38), residues: 140

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 1159)
  covalent geometry    : angle       0.62215 ( 1611)
  hydrogen bonds       : bond        0.04599 (   36)
  hydrogen bonds       : angle       6.03635 (  105)

*********************** 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  : 0.024 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0041
  time to fit residues: 0.0558
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  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:   40.0000
   chunk 19 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:   40.0000
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:   40.0000
   chunk 8 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   overall best weight:    5.1588

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.091971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.079313 restraints weight = 8409.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.079662 restraints weight = 7720.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.079831 restraints weight = 7082.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.080010 restraints weight = 6735.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.080010 restraints weight = 6449.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.8652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   1159  Z= 0.199
  Angle     :  0.626   4.614   1611  Z= 0.378
  Chirality :  0.049   0.132    221
  Planarity :  0.003   0.010    233
  Dihedral  :  6.309  18.367    233
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.69 (0.46), residues: 231
  helix: -3.88 (0.51), residues: 33
  sheet: -2.37 (0.80), residues: 45
  loop : -3.38 (0.42), residues: 153

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 1159)
  covalent geometry    : angle       0.62598 ( 1611)
  hydrogen bonds       : bond        0.05012 (   36)
  hydrogen bonds       : angle       5.89045 (  105)

*********************** 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  : 0.024 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0043
  time to fit residues: 0.0587
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  : 0.024 
-------------------------------------------------------------------------------
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:   50.0000
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 16 optimal weight:   40.0000
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0970
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:   30.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    4.6186

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.092463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.079704 restraints weight = 8384.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.079897 restraints weight = 7672.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.080072 restraints weight = 7226.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.080077 restraints weight = 6962.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.080077 restraints weight = 6949.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6090
moved from start:          0.9707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   1159  Z= 0.159
  Angle     :  0.556   3.710   1611  Z= 0.333
  Chirality :  0.048   0.119    221
  Planarity :  0.002   0.009    233
  Dihedral  :  5.603  21.479    233
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.62 (0.50), residues: 231
  helix: -3.32 (0.61), residues: 33
  sheet: -2.45 (0.67), residues: 66
  loop : -3.44 (0.48), residues: 132

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 1159)
  covalent geometry    : angle       0.55609 ( 1611)
  hydrogen bonds       : bond        0.03557 (   36)
  hydrogen bonds       : angle       5.32975 (  105)

*********************** 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  : 0.037 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0070
  time to fit residues: 0.0863
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  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 9 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 14 optimal weight:   40.0000
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:   30.0000
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   overall best weight:   14.7996

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.085761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.074113 restraints weight = 8527.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.074484 restraints weight = 7781.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.074719 restraints weight = 7230.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.074800 restraints weight = 6888.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.074889 restraints weight = 6700.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6351
moved from start:          1.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   1159  Z= 0.415
  Angle     :  1.089  10.426   1611  Z= 0.644
  Chirality :  0.054   0.139    221
  Planarity :  0.007   0.022    233
  Dihedral  :  9.811  28.805    233
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 25.54 %
    Favored  : 74.03 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.92 (0.44), residues: 231
  helix: -3.83 (0.55), residues: 33
  sheet: -3.13 (0.66), residues: 55
  loop : -4.56 (0.41), residues: 143

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 1159)
  covalent geometry    : angle       1.08917 ( 1611)
  hydrogen bonds       : bond        0.06048 (   36)
  hydrogen bonds       : angle       8.78572 (  105)

*********************** 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  : 0.025 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0046
  time to fit residues: 0.0578
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  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   overall best weight:    7.5592

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.085640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.074684 restraints weight = 8429.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.074906 restraints weight = 7407.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.075108 restraints weight = 6712.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.075108 restraints weight = 6352.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.075108 restraints weight = 6352.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          1.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1159  Z= 0.225
  Angle     :  0.715   5.715   1611  Z= 0.425
  Chirality :  0.049   0.125    221
  Planarity :  0.004   0.013    233
  Dihedral  :  7.595  26.474    233
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.18 %
    Favored  : 81.82 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.57 (0.46), residues: 231
  helix: -3.06 (0.74), residues: 32
  sheet: -3.45 (0.65), residues: 57
  loop : -4.19 (0.42), residues: 142

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 1159)
  covalent geometry    : angle       0.71530 ( 1611)
  hydrogen bonds       : bond        0.03844 (   36)
  hydrogen bonds       : angle       7.00120 (  105)

*********************** 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  : 0.050 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0077
  time to fit residues: 0.1051
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  : 0.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 16 optimal weight:   50.0000
   chunk 5 optimal weight:   30.0000
   chunk 19 optimal weight:   30.0000
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 18 optimal weight:   30.0000
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:   10.3994

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.082597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072319 restraints weight = 8713.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072319 restraints weight = 7707.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072319 restraints weight = 7707.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072319 restraints weight = 7707.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072319 restraints weight = 7707.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          1.4231

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= 0.309
  Angle     :  0.904   8.025   1611  Z= 0.540
  Chirality :  0.051   0.129    221
  Planarity :  0.005   0.018    233
  Dihedral  :  9.186  29.657    233
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.57 %
    Favored  : 71.43 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.90 (0.45), residues: 231
  helix: -3.22 (0.69), residues: 32
  sheet: -3.56 (0.78), residues: 44
  loop : -4.50 (0.39), residues: 155

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 1159)
  covalent geometry    : angle       0.90440 ( 1611)
  hydrogen bonds       : bond        0.05042 (   36)
  hydrogen bonds       : angle       8.34737 (  105)

*********************** 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  : 0.051 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0078
  time to fit residues: 0.1145
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  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 6 optimal weight:   20.0000
   overall best weight:    5.2988

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.084418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.073396 restraints weight = 8616.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.073930 restraints weight = 7493.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.074127 restraints weight = 6764.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.074448 restraints weight = 6344.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 12)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.074447 restraints weight = 6031.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          1.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1159  Z= 0.168
  Angle     :  0.654   6.613   1611  Z= 0.389
  Chirality :  0.048   0.123    221
  Planarity :  0.003   0.010    233
  Dihedral  :  7.382  25.783    233
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.67 (0.45), residues: 231
  helix: -3.01 (0.71), residues: 32
  sheet: -3.77 (0.70), residues: 49
  loop : -4.20 (0.41), residues: 150

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 1159)
  covalent geometry    : angle       0.65433 ( 1611)
  hydrogen bonds       : bond        0.03508 (   36)
  hydrogen bonds       : angle       6.79354 (  105)

*********************** 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  : 0.044 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0069
  time to fit residues: 0.1003
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  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 6 optimal weight:   30.0000
   chunk 4 optimal weight:   30.0000
   chunk 14 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   overall best weight:    8.9994

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.082458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.071733 restraints weight = 8756.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 16)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.071978 restraints weight = 7492.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.072503 restraints weight = 6886.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.072698 restraints weight = 6320.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.072756 restraints weight = 6010.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          1.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   1159  Z= 0.259
  Angle     :  0.809   8.041   1611  Z= 0.483
  Chirality :  0.050   0.129    221
  Planarity :  0.004   0.015    233
  Dihedral  :  8.580  26.850    233
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.81
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.83 (0.45), residues: 231
  helix: -3.48 (0.71), residues: 31
  sheet: -3.02 (0.97), residues: 34
  loop : -4.52 (0.38), residues: 166

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 1159)
  covalent geometry    : angle       0.80904 ( 1611)
  hydrogen bonds       : bond        0.04418 (   36)
  hydrogen bonds       : angle       7.97690 (  105)

*********************** 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  : 0.042 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0070
  time to fit residues: 0.0992
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  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   chunk 21 optimal weight:   50.0000
   chunk 18 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   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 = 0.3677 r_free = 0.3677 target = 0.081290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.070744 restraints weight = 8598.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.071365 restraints weight = 7072.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.071836 restraints weight = 6180.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.072131 restraints weight = 5608.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.072219 restraints weight = 5265.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6449
moved from start:          1.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   1159  Z= 0.321
  Angle     :  0.903   8.511   1611  Z= 0.543
  Chirality :  0.051   0.122    221
  Planarity :  0.005   0.015    233
  Dihedral  :  9.900  28.795    233
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.84 %
    Favored  : 73.16 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.07 (0.45), residues: 231
  helix: -3.91 (0.64), residues: 31
  sheet: -3.65 (0.75), residues: 45
  loop : -4.50 (0.41), residues: 155

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 1159)
  covalent geometry    : angle       0.90266 ( 1611)
  hydrogen bonds       : bond        0.04943 (   36)
  hydrogen bonds       : angle       8.40752 (  105)

********************** 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  : 0.045 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0072
  time to fit residues: 0.1037
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  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 23
   random chunks:
   chunk 21 optimal weight:   50.0000
   chunk 7 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   overall best weight:    8.3994

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.080827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.070749 restraints weight = 8576.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.071299 restraints weight = 7294.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.071679 restraints weight = 6480.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.071827 restraints weight = 5960.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.072066 restraints weight = 5698.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          1.5611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   1159  Z= 0.238
  Angle     :  0.759   7.349   1611  Z= 0.456
  Chirality :  0.049   0.121    221
  Planarity :  0.004   0.012    233
  Dihedral  :  8.658  26.382    233
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.81 %
    Favored  : 76.19 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.12 (0.46), residues: 231
  helix: -3.91 (0.61), residues: 32
  sheet: -3.53 (0.72), residues: 57
  loop : -4.58 (0.42), residues: 142

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 1159)
  covalent geometry    : angle       0.75877 ( 1611)
  hydrogen bonds       : bond        0.03878 (   36)
  hydrogen bonds       : angle       7.76333 (  105)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 339.27 seconds
wall clock time: 6 minutes 54.92 seconds (414.92 seconds total)