Starting phenix.real_space_refine
on Wed Sep 17 04:00:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mel_48217/09_2025/9mel_48217.cif"
  }
  resolution = 3.17
  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=  -0.001 sd=   0.049
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: 6
    Type Number    sf(0)   Gaussians
     K       3      8.98       5
     S      14      5.16       5
     C    2410      2.51       5
     N     562      2.21       5
     O     596      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3589
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
      Conformer: "B"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
          bond proxies already assigned to first conformer: 1788
    Chain: "B"
      Number of atoms: 1759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
      Conformer: "B"
        Number of residues, atoms: 238, 1754
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 228}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
          bond proxies already assigned to first conformer: 1788
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 68
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 34
          Unusual residues: {'1II': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 34
          Unusual residues: {'1II': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C07A1II B 401 " occ=0.50
      ... (66 atoms not shown)
      pdb=" O03B1II B 401 " occ=0.50
  Time building chain proxies: 1.96, per 1000 atoms: 0.55
  Number of scatterers: 3589
  At special positions: 0
  Unit cell: (71.775, 61.625, 88.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       3     19.00
     S      14     16.00
     F       4      9.00
     O     596      8.00
     N     562      7.00
     C    2410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS B  53 " distance=2.03

  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: 0.40
  Conformation dependent library (CDL) restraints added in 335.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  892

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 51
      Proline residue:  A  31  - end of helix
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 72 through 78
      removed outlier: 4.171A  pdb=" N   VAL A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 116 through 150
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 167 through 195
      removed outlier: 3.604A  pdb=" N   TRP A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   LEU A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   VAL A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 200 through 213
    Processing helix  chain 'A' and resid 230 through 263
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'B' and resid 8 through 51
      Proline residue:  B  31  - end of helix
    Processing helix  chain 'B' and resid 55 through 69
    Processing helix  chain 'B' and resid 72 through 78
      removed outlier: 4.171A  pdb=" N   VAL B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 105
    Processing helix  chain 'B' and resid 116 through 150
      Proline residue:  B 132  - end of helix
    Processing helix  chain 'B' and resid 200 through 213
    Processing helix  chain 'B' and resid 230 through 263
    Processing helix  chain 'B' and resid 266 through 271

    280 hydrogen bonds defined for protein.
    838 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: 0.56

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1066
        1.34 -     1.46: 840
        1.46 -     1.58: 1750
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3676
  Sorted by residual:
  bond pdb=" C31B1II B 401 "
       pdb=" C33B1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.350  0.028 2.00e-02 2.50e+03 1.99e+00
  bond pdb=" C31A1II B 401 "
       pdb=" C33A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.378  1.351  0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C07A1II B 401 "
       pdb=" C09A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.546  1.521  0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" C07B1II B 401 "
       pdb=" C09B1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.546  1.521  0.025 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C30A1II B 401 "
       pdb=" C34A1II B 401 "
    ideal  model  delta    sigma   weight residual
    1.383  1.360  0.023 2.00e-02 2.50e+03 1.31e+00
  ... (remaining 3671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 4891
        1.73 -     3.46: 110
        3.46 -     5.19: 33
        5.19 -     6.92: 7
        6.92 -     8.64: 5
  Bond angle restraints: 5046
  Sorted by residual:
  angle pdb=" C20B1II B 401 "
        pdb=" C17B1II B 401 "
        pdb=" C21B1II B 401 "
      ideal   model   delta    sigma   weight residual
     110.45  119.09   -8.64 3.00e+00 1.11e-01 8.30e+00
  angle pdb=" C20A1II B 401 "
        pdb=" C17A1II B 401 "
        pdb=" C21A1II B 401 "
      ideal   model   delta    sigma   weight residual
     110.45  118.50   -8.05 3.00e+00 1.11e-01 7.20e+00
  angle pdb=" C   LEU B 265 "
        pdb=" N   THR B 266 "
        pdb=" CA  THR B 266 "
      ideal   model   delta    sigma   weight residual
     121.54  126.54   -5.00 1.91e+00 2.74e-01 6.85e+00
  angle pdb=" C   LEU A 265 "
        pdb=" N   THR A 266 "
        pdb=" CA  THR A 266 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.78e+00
  angle pdb=" C   THR B 105 "
        pdb=" N   THR B 106 "
        pdb=" CA  THR B 106 "
      ideal   model   delta    sigma   weight residual
     122.08  125.67   -3.59 1.47e+00 4.63e-01 5.96e+00
  ... (remaining 5041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.02: 2015
       31.02 -    62.04: 87
       62.04 -    93.06: 11
       93.06 -   124.08: 4
      124.08 -   155.10: 6
  Dihedral angle restraints: 2123
    sinusoidal: 739
      harmonic: 1384
  Sorted by residual:
  dihedral pdb=" C15A1II B 401 "
           pdb=" C12A1II B 401 "
           pdb=" C13A1II B 401 "
           pdb=" N04A1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     187.89   32.79  155.10     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" C11B1II B 401 "
           pdb=" C12B1II B 401 "
           pdb=" N04B1II B 401 "
           pdb=" C13B1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.54   88.01 -146.55     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C11A1II B 401 "
           pdb=" C12A1II B 401 "
           pdb=" N04A1II B 401 "
           pdb=" C13A1II B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.54   82.41 -140.95     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 2120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 626
       0.109 -    0.218: 8
       0.218 -    0.327: 0
       0.327 -    0.436: 0
       0.436 -    0.545: 2
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" C07B1II B 401 "
            pdb=" C08B1II B 401 "
            pdb=" C09B1II B 401 "
            pdb=" N05B1II B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.77   -0.55 2.00e-01 2.50e+01 7.44e+00
  chirality pdb=" C07A1II B 401 "
            pdb=" C08A1II B 401 "
            pdb=" C09A1II B 401 "
            pdb=" N05A1II B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.82   -0.49 2.00e-01 2.50e+01 6.03e+00
  chirality pdb=" CA  THR A 214 "
            pdb=" N   THR A 214 "
            pdb=" C   THR A 214 "
            pdb=" CB  THR A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 633 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 266 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   THR A 266 "    0.035 2.00e-02 2.50e+03
        pdb=" O   THR A 266 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A 267 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 266 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   THR B 266 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   THR B 266 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B 267 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 181 "   -0.005 2.00e-02 2.50e+03   1.02e-02 1.03e+00
        pdb=" C   VAL B 181 "    0.018 2.00e-02 2.50e+03
        pdb=" O   VAL B 181 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   THR B 182 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.79: 857
        2.79 -     3.38: 4311
        3.38 -     3.97: 6823
        3.97 -     4.55: 9414
        4.55 -     5.14: 13336
  Nonbonded interactions: 34741
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 108 "
            pdb=" K     K A 401 "
     model   vdw
     2.206 2.850
  nonbonded pdb=" O   GLY B 108 "
            pdb=" K     K A 401 "
     model   vdw
     2.218 2.850
  nonbonded pdb=" O   GLY B 216 "
            pdb=" K     K A 401 "
     model   vdw
     2.362 2.850
  nonbonded pdb=" O   GLY A 216 "
            pdb=" K     K A 401 "
     model   vdw
     2.378 2.850
  nonbonded pdb=" O   SER B 213 "
            pdb=" OG1 THR B 214 "
     model   vdw
     2.566 3.040
  ... (remaining 34736 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 134 or resid 136 through 271))
  selection = (chain 'B' and (resid 7 through 134 or resid 136 through 271))
}

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=0.47 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.150
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.110
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3677  Z= 0.192
  Angle     :  0.733   8.644   5048  Z= 0.337
  Chirality :  0.047   0.545    636
  Planarity :  0.003   0.024    600
  Dihedral  : 20.720 155.097   1228
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.82 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.40 (0.40), residues: 466
  helix:  2.98 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.07 (0.80), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 144 
 TYR   0.010   0.002   TYR B 206 
 PHE   0.013   0.002   PHE A 122 
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3676)
  covalent geometry    : angle       0.73350 ( 5046)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.02827 (    2)
  hydrogen bonds       : bond        0.10239 (  280)
  hydrogen bonds       : angle       4.74274 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8165 (tp) cc_final: 0.7552 (mt)
REVERT: A   64 GLU cc_start: 0.8263 (tp30) cc_final: 0.7613 (mt-10)
REVERT: A  144 ARG cc_start: 0.6391 (mtt180) cc_final: 0.5868 (mmm160)
REVERT: A  237 LEU cc_start: 0.8110 (mm) cc_final: 0.7705 (mm)
REVERT: A  257 ARG cc_start: 0.7644 (ttp80) cc_final: 0.6559 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8154 (tp) cc_final: 0.7540 (mt)
REVERT: B   64 GLU cc_start: 0.8261 (tp30) cc_final: 0.7607 (mt-10)
REVERT: B  144 ARG cc_start: 0.6345 (mtt180) cc_final: 0.5842 (mmm160)
REVERT: B  237 LEU cc_start: 0.8103 (mm) cc_final: 0.7697 (mm)
REVERT: B  257 ARG cc_start: 0.7643 (ttp80) cc_final: 0.6558 (tpp-160)
  outliers start: 6
  outliers final: 6
  residues processed: 54
  average time/residue: 0.1515
  time to fit residues: 9.1369
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.177659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.133771 restraints weight = 10935.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 4.06
r_work: 0.3103 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.0504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3677  Z= 0.145
  Angle     :  0.627  10.061   5048  Z= 0.289
  Chirality :  0.037   0.194    636
  Planarity :  0.003   0.024    600
  Dihedral  : 19.765 132.159    570
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.68 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.79 (0.41), residues: 466
  helix:  3.18 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.69 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  27 
 TYR   0.010   0.002   TYR B 234 
 PHE   0.013   0.002   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3676)
  covalent geometry    : angle       0.62680 ( 5046)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.18807 (    2)
  hydrogen bonds       : bond        0.03080 (  280)
  hydrogen bonds       : angle       3.67535 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8152 (tp) cc_final: 0.7529 (mt)
REVERT: A  144 ARG cc_start: 0.6316 (mtt180) cc_final: 0.5867 (mmm160)
REVERT: A  237 LEU cc_start: 0.8116 (mm) cc_final: 0.7711 (mm)
REVERT: A  257 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6520 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8130 (tp) cc_final: 0.7505 (mt)
REVERT: B  144 ARG cc_start: 0.6307 (mtt180) cc_final: 0.5869 (mmm160)
REVERT: B  237 LEU cc_start: 0.8090 (mm) cc_final: 0.7687 (mm)
REVERT: B  257 ARG cc_start: 0.7616 (ttp80) cc_final: 0.6523 (tpp-160)
  outliers start: 7
  outliers final: 3
  residues processed: 57
  average time/residue: 0.1409
  time to fit residues: 9.0833
Evaluate side-chains
  51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.176313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.132518 restraints weight = 8533.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.38
r_work: 0.3125 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.0752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3677  Z= 0.149
  Angle     :  0.626  10.373   5048  Z= 0.287
  Chirality :  0.037   0.169    636
  Planarity :  0.003   0.025    600
  Dihedral  : 19.449 134.104    562
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.95 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.89 (0.41), residues: 466
  helix:  3.26 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.70 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  65 
 TYR   0.012   0.002   TYR B 234 
 PHE   0.013   0.002   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3676)
  covalent geometry    : angle       0.62636 ( 5046)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.20531 (    2)
  hydrogen bonds       : bond        0.03027 (  280)
  hydrogen bonds       : angle       3.44454 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8126 (tp) cc_final: 0.7516 (mt)
REVERT: A  144 ARG cc_start: 0.6350 (mtt180) cc_final: 0.5892 (mmm160)
REVERT: A  237 LEU cc_start: 0.8109 (mm) cc_final: 0.7701 (mm)
REVERT: A  257 ARG cc_start: 0.7624 (ttp80) cc_final: 0.6522 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8132 (tp) cc_final: 0.7515 (mt)
REVERT: B  144 ARG cc_start: 0.6387 (mtt180) cc_final: 0.5961 (mmm160)
REVERT: B  237 LEU cc_start: 0.8100 (mm) cc_final: 0.7693 (mm)
REVERT: B  257 ARG cc_start: 0.7620 (ttp80) cc_final: 0.6516 (tpp-160)
  outliers start: 10
  outliers final: 7
  residues processed: 59
  average time/residue: 0.1355
  time to fit residues: 9.0262
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.176562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132995 restraints weight = 8419.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 3.35
r_work: 0.3102 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3677  Z= 0.182
  Angle     :  0.656  10.876   5048  Z= 0.302
  Chirality :  0.038   0.157    636
  Planarity :  0.003   0.024    600
  Dihedral  : 19.585 136.338    562
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.82 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.69 (0.41), residues: 466
  helix:  3.11 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.72 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  37 
 TYR   0.015   0.002   TYR B 234 
 PHE   0.014   0.002   PHE A 122 
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 3676)
  covalent geometry    : angle       0.65654 ( 5046)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.15250 (    2)
  hydrogen bonds       : bond        0.03138 (  280)
  hydrogen bonds       : angle       3.44188 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8203 (tp) cc_final: 0.7560 (mt)
REVERT: A  144 ARG cc_start: 0.6380 (mtt180) cc_final: 0.5917 (mmm160)
REVERT: A  237 LEU cc_start: 0.8143 (mm) cc_final: 0.7728 (mm)
REVERT: A  257 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6495 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8187 (tp) cc_final: 0.7550 (mt)
REVERT: B  144 ARG cc_start: 0.6381 (mtt180) cc_final: 0.5928 (mmm160)
REVERT: B  237 LEU cc_start: 0.8138 (mm) cc_final: 0.7728 (mm)
REVERT: B  257 ARG cc_start: 0.7603 (ttp80) cc_final: 0.6507 (tpp-160)
  outliers start: 7
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1444
  time to fit residues: 9.4332
Evaluate side-chains
  59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0040
   chunk 45 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.1992

-------------------------------------------------------------------------------
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 = 0.178952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.136486 restraints weight = 13382.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 4.27
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3677  Z= 0.109
  Angle     :  0.621   9.741   5048  Z= 0.275
  Chirality :  0.035   0.118    636
  Planarity :  0.003   0.026    600
  Dihedral  : 17.796 119.876    562
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.24 %
    Favored  : 80.75 %
  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:  4.10 (0.41), residues: 466
  helix:  3.43 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.72 (0.85), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  44 
 TYR   0.010   0.001   TYR B 206 
 PHE   0.008   0.001   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3676)
  covalent geometry    : angle       0.62102 ( 5046)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.23331 (    2)
  hydrogen bonds       : bond        0.02646 (  280)
  hydrogen bonds       : angle       3.21141 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8132 (tp) cc_final: 0.7519 (mt)
REVERT: A  144 ARG cc_start: 0.6289 (mtt180) cc_final: 0.6011 (mmm160)
REVERT: A  237 LEU cc_start: 0.8144 (mm) cc_final: 0.7746 (mm)
REVERT: A  257 ARG cc_start: 0.7313 (ttp80) cc_final: 0.6552 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8148 (tp) cc_final: 0.7542 (mt)
REVERT: B  144 ARG cc_start: 0.6351 (mtt180) cc_final: 0.6090 (mmm160)
REVERT: B  237 LEU cc_start: 0.8117 (mm) cc_final: 0.7721 (mm)
REVERT: B  257 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6578 (tpp-160)
  outliers start: 7
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1505
  time to fit residues: 9.4699
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.180875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.140115 restraints weight = 12071.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 3.99
r_work: 0.3076 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3677  Z= 0.134
  Angle     :  0.625  10.764   5048  Z= 0.282
  Chirality :  0.035   0.123    636
  Planarity :  0.003   0.025    600
  Dihedral  : 18.177 124.150    562
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.10 %
    Favored  : 80.46 %
  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:  4.05 (0.41), residues: 466
  helix:  3.39 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.72 (0.85), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  44 
 TYR   0.009   0.001   TYR A 206 
 PHE   0.012   0.002   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3676)
  covalent geometry    : angle       0.62496 ( 5046)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.23071 (    2)
  hydrogen bonds       : bond        0.02801 (  280)
  hydrogen bonds       : angle       3.17778 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8208 (tp) cc_final: 0.7588 (mt)
REVERT: A  144 ARG cc_start: 0.6494 (mtt180) cc_final: 0.5994 (mmm160)
REVERT: A  237 LEU cc_start: 0.8184 (mm) cc_final: 0.7791 (mm)
REVERT: A  257 ARG cc_start: 0.7689 (ttp80) cc_final: 0.6585 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8194 (tp) cc_final: 0.7580 (mt)
REVERT: B  144 ARG cc_start: 0.6473 (mtt180) cc_final: 0.6040 (mmm160)
REVERT: B  237 LEU cc_start: 0.8187 (mm) cc_final: 0.7800 (mm)
REVERT: B  257 ARG cc_start: 0.7688 (ttp80) cc_final: 0.6575 (tpp-160)
  outliers start: 5
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1492
  time to fit residues: 9.1981
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  183 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.2980
   chunk 18 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.179970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.135440 restraints weight = 11064.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 3.90
r_work: 0.3122 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3677  Z= 0.134
  Angle     :  0.634  11.124   5048  Z= 0.285
  Chirality :  0.035   0.125    636
  Planarity :  0.003   0.025    600
  Dihedral  : 17.819 121.759    562
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.39 %
    Favored  : 79.89 %
  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:  4.06 (0.41), residues: 466
  helix:  3.39 (0.25), residues: 376
  sheet:  None (None), residues: 0
  loop : -0.71 (0.86), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 144 
 TYR   0.010   0.001   TYR B 234 
 PHE   0.012   0.001   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3676)
  covalent geometry    : angle       0.63388 ( 5046)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.20428 (    2)
  hydrogen bonds       : bond        0.02781 (  280)
  hydrogen bonds       : angle       3.17527 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8186 (tp) cc_final: 0.7573 (mt)
REVERT: A  144 ARG cc_start: 0.6477 (mtt180) cc_final: 0.6001 (mmm160)
REVERT: A  237 LEU cc_start: 0.8191 (mm) cc_final: 0.7807 (mm)
REVERT: A  257 ARG cc_start: 0.7677 (ttp80) cc_final: 0.6579 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8180 (tp) cc_final: 0.7571 (mt)
REVERT: B  144 ARG cc_start: 0.6449 (mtt180) cc_final: 0.6038 (mmm160)
REVERT: B  237 LEU cc_start: 0.8188 (mm) cc_final: 0.7808 (mm)
REVERT: B  257 ARG cc_start: 0.7667 (ttp80) cc_final: 0.6598 (tpp-160)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1519
  time to fit residues: 9.3979
Evaluate side-chains
  56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  183 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0980
   chunk 18 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.3338

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.181836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137429 restraints weight = 9989.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.42
r_work: 0.3150 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3677  Z= 0.120
  Angle     :  0.637  10.755   5048  Z= 0.281
  Chirality :  0.035   0.195    636
  Planarity :  0.003   0.026    600
  Dihedral  : 15.830 110.065    562
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.10 %
    Favored  : 79.60 %
  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:  4.04 (0.40), residues: 466
  helix:  3.27 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.68 (0.89), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  44 
 TYR   0.009   0.001   TYR B 206 
 PHE   0.010   0.001   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3676)
  covalent geometry    : angle       0.63748 ( 5046)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.22486 (    2)
  hydrogen bonds       : bond        0.02663 (  280)
  hydrogen bonds       : angle       3.07574 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8169 (tp) cc_final: 0.7571 (mt)
REVERT: A  144 ARG cc_start: 0.6442 (mtt180) cc_final: 0.5998 (mmm160)
REVERT: A  237 LEU cc_start: 0.8128 (mm) cc_final: 0.7755 (mm)
REVERT: A  257 ARG cc_start: 0.7643 (ttp80) cc_final: 0.6590 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8156 (tp) cc_final: 0.7558 (mt)
REVERT: B  144 ARG cc_start: 0.6466 (mtt180) cc_final: 0.6067 (mmm160)
REVERT: B  237 LEU cc_start: 0.8104 (mm) cc_final: 0.7734 (mm)
REVERT: B  257 ARG cc_start: 0.7637 (ttp80) cc_final: 0.6456 (mmt-90)
  outliers start: 8
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1434
  time to fit residues: 9.2277
Evaluate side-chains
  60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  270 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.179721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137293 restraints weight = 7949.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.18
r_work: 0.3118 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3677  Z= 0.187
  Angle     :  0.634   8.330   5048  Z= 0.296
  Chirality :  0.038   0.199    636
  Planarity :  0.004   0.024    600
  Dihedral  : 15.377 108.159    562
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.83 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.75 (0.40), residues: 466
  helix:  3.06 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.71 (0.90), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  37 
 TYR   0.015   0.002   TYR B 234 
 PHE   0.014   0.002   PHE A 122 
 TRP   0.008   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 3676)
  covalent geometry    : angle       0.63377 ( 5046)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.11741 (    2)
  hydrogen bonds       : bond        0.03003 (  280)
  hydrogen bonds       : angle       3.27518 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8214 (tp) cc_final: 0.7589 (mt)
REVERT: A  144 ARG cc_start: 0.6498 (mtt180) cc_final: 0.6023 (mmm160)
REVERT: A  237 LEU cc_start: 0.8176 (mm) cc_final: 0.7782 (mm)
REVERT: A  257 ARG cc_start: 0.7598 (ttp80) cc_final: 0.6562 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8208 (tp) cc_final: 0.7575 (mt)
REVERT: B  144 ARG cc_start: 0.6432 (mtt180) cc_final: 0.6022 (mmm160)
REVERT: B  237 LEU cc_start: 0.8184 (mm) cc_final: 0.7797 (mm)
REVERT: B  257 ARG cc_start: 0.7591 (ttp80) cc_final: 0.6561 (tpp-160)
  outliers start: 5
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1440
  time to fit residues: 8.8337
Evaluate side-chains
  57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0770
   chunk 35 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.179545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.135773 restraints weight = 11649.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 3.91
r_work: 0.3097 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3677  Z= 0.145
  Angle     :  0.576   9.171   5048  Z= 0.272
  Chirality :  0.036   0.127    636
  Planarity :  0.003   0.025    600
  Dihedral  : 11.947  92.077    562
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.54 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.88 (0.40), residues: 466
  helix:  3.15 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.69 (0.90), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  65 
 TYR   0.011   0.002   TYR B 234 
 PHE   0.012   0.001   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3676)
  covalent geometry    : angle       0.57596 ( 5046)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.22815 (    2)
  hydrogen bonds       : bond        0.02809 (  280)
  hydrogen bonds       : angle       3.22036 (  838)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8156 (tp) cc_final: 0.7552 (mt)
REVERT: A  144 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5979 (mmm160)
REVERT: A  237 LEU cc_start: 0.8131 (mm) cc_final: 0.7741 (mm)
REVERT: A  257 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6527 (tpp-160)
REVERT: B   20 LEU cc_start: 0.8154 (tp) cc_final: 0.7545 (mt)
REVERT: B  144 ARG cc_start: 0.6438 (mtt180) cc_final: 0.6025 (mmm160)
REVERT: B  237 LEU cc_start: 0.8129 (mm) cc_final: 0.7739 (mm)
REVERT: B  257 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6536 (tpp-160)
  outliers start: 6
  outliers final: 6
  residues processed: 55
  average time/residue: 0.1470
  time to fit residues: 9.1040
Evaluate side-chains
  58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  270 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.179051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.134956 restraints weight = 10896.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 3.90
r_work: 0.3096 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3677  Z= 0.155
  Angle     :  0.569   5.388   5048  Z= 0.277
  Chirality :  0.036   0.128    636
  Planarity :  0.003   0.025    600
  Dihedral  :  9.139  76.813    562
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.83 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.79 (0.40), residues: 466
  helix:  3.09 (0.25), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.70 (0.90), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 144 
 TYR   0.014   0.002   TYR B 234 
 PHE   0.014   0.002   PHE A 122 
 TRP   0.007   0.001   TRP A 171 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3676)
  covalent geometry    : angle       0.56872 ( 5046)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       0.15755 (    2)
  hydrogen bonds       : bond        0.02895 (  280)
  hydrogen bonds       : angle       3.23830 (  838)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1411.04 seconds
wall clock time: 24 minutes 51.66 seconds (1491.66 seconds total)