Starting phenix.real_space_refine
on Tue Aug  4 12:25:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/20yj_67393/08_2026/20yj_67393_neut.cif"
  }
  resolution = 3.4
  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=   1.000
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    1740      2.51       5
     N     430      2.21       5
     O     420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2590
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 259
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 31}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.51, per 1000 atoms: 0.20
  Number of scatterers: 2590
  At special positions: 0
  Unit cell: (75.492, 66.172, 43.804, 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     420      8.00
     N     430      7.00
     C    1740      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: 0.20
  Conformation dependent library (CDL) restraints added in 97.6 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  620

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110
      removed outlier: 6.879A  pdb=" N   LEU A 109 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU C 109 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU E 109 " --> pdb=" O   VAL G 110 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU G 109 " --> pdb=" O   VAL I 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 130
      removed outlier: 6.688A  pdb=" N   ASP C 128 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE A 129 " --> pdb=" O   ASP C 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN C 130 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASP E 128 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE C 129 " --> pdb=" O   ASP E 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN E 130 " --> pdb=" O   PHE C 129 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ASP G 128 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE E 129 " --> pdb=" O   ASP G 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN G 130 " --> pdb=" O   PHE E 129 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ASP I 128 " --> pdb=" O   ALA G 127 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   PHE G 129 " --> pdb=" O   ASP I 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN I 130 " --> pdb=" O   PHE G 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 110
      removed outlier: 6.879A  pdb=" N   LEU B 109 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LEU D 109 " --> pdb=" O   VAL F 110 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU F 109 " --> pdb=" O   VAL H 110 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LEU H 109 " --> pdb=" O   VAL J 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 130
      removed outlier: 6.688A  pdb=" N   ASP D 128 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   PHE B 129 " --> pdb=" O   ASP D 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN D 130 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASP F 128 " --> pdb=" O   ALA D 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE D 129 " --> pdb=" O   ASP F 128 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN F 130 " --> pdb=" O   PHE D 129 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASP H 128 " --> pdb=" O   ALA F 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE F 129 " --> pdb=" O   ASP H 128 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   GLN H 130 " --> pdb=" O   PHE F 129 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASP J 128 " --> pdb=" O   ALA H 127 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE H 129 " --> pdb=" O   ASP J 128 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   GLN J 130 " --> pdb=" O   PHE H 129 " (cutoff:3.500A)

    24 hydrogen bonds defined for protein.
    72 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: 0.32

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 410
        1.28 -     1.35: 390
        1.35 -     1.41: 240
        1.41 -     1.48: 370
        1.48 -     1.54: 1220
  Bond restraints: 2630
  Sorted by residual:
  bond pdb=" CG  LEU F 109 "
       pdb=" CD1 LEU F 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.08e+00
  bond pdb=" CG  LEU E 109 "
       pdb=" CD1 LEU E 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.02e+00
  bond pdb=" CG  LEU B 109 "
       pdb=" CD1 LEU B 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.00e+00
  bond pdb=" CG  LEU I 109 "
       pdb=" CD1 LEU I 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 3.98e+00
  bond pdb=" CG  LEU A 109 "
       pdb=" CD1 LEU A 109 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 3.98e+00
  ... (remaining 2625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 3237
        1.84 -     3.68: 254
        3.68 -     5.52: 29
        5.52 -     7.36: 10
        7.36 -     9.21: 20
  Bond angle restraints: 3550
  Sorted by residual:
  angle pdb=" CB  LEU I 109 "
        pdb=" CG  LEU I 109 "
        pdb=" CD1 LEU I 109 "
      ideal   model   delta    sigma   weight residual
     110.70  101.49    9.21 3.00e+00 1.11e-01 9.42e+00
  angle pdb=" CB  LEU D 109 "
        pdb=" CG  LEU D 109 "
        pdb=" CD1 LEU D 109 "
      ideal   model   delta    sigma   weight residual
     110.70  101.53    9.17 3.00e+00 1.11e-01 9.34e+00
  angle pdb=" CB  LEU C 109 "
        pdb=" CG  LEU C 109 "
        pdb=" CD1 LEU C 109 "
      ideal   model   delta    sigma   weight residual
     110.70  101.53    9.17 3.00e+00 1.11e-01 9.34e+00
  angle pdb=" CB  LEU H 109 "
        pdb=" CG  LEU H 109 "
        pdb=" CD1 LEU H 109 "
      ideal   model   delta    sigma   weight residual
     110.70  101.53    9.17 3.00e+00 1.11e-01 9.34e+00
  angle pdb=" CB  LEU B 109 "
        pdb=" CG  LEU B 109 "
        pdb=" CD1 LEU B 109 "
      ideal   model   delta    sigma   weight residual
     110.70  101.54    9.16 3.00e+00 1.11e-01 9.32e+00
  ... (remaining 3545 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 1237
       15.05 -    30.10: 203
       30.10 -    45.16: 100
       45.16 -    60.21: 0
       60.21 -    75.26: 10
  Dihedral angle restraints: 1550
    sinusoidal: 610
      harmonic: 940
  Sorted by residual:
  dihedral pdb=" CA  GLN G 130 "
           pdb=" C   GLN G 130 "
           pdb=" N   LYS G 131 "
           pdb=" CA  LYS G 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.64  -15.36     0      5.00e+00 4.00e-02 9.44e+00
  dihedral pdb=" CA  GLN C 130 "
           pdb=" C   GLN C 130 "
           pdb=" N   LYS C 131 "
           pdb=" CA  LYS C 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.68  -15.32     0      5.00e+00 4.00e-02 9.39e+00
  dihedral pdb=" CA  GLN J 130 "
           pdb=" C   GLN J 130 "
           pdb=" N   LYS J 131 "
           pdb=" CA  LYS J 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.68  -15.32     0      5.00e+00 4.00e-02 9.39e+00
  ... (remaining 1547 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 213
       0.026 -    0.053: 77
       0.053 -    0.079: 90
       0.079 -    0.105: 29
       0.105 -    0.131: 31
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CB  VAL H 133 "
            pdb=" CA  VAL H 133 "
            pdb=" CG1 VAL H 133 "
            pdb=" CG2 VAL H 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CB  VAL G 133 "
            pdb=" CA  VAL G 133 "
            pdb=" CG1 VAL G 133 "
            pdb=" CG2 VAL G 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CB  VAL J 133 "
            pdb=" CA  VAL J 133 "
            pdb=" CG1 VAL J 133 "
            pdb=" CG2 VAL J 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 437 not shown)

  Planarity restraints: 440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 121 "   -0.009 2.00e-02 2.50e+03   9.86e-03 1.70e+00
        pdb=" CG  PHE B 121 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 121 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 121 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 121 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 121 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I 121 "    0.009 2.00e-02 2.50e+03   9.85e-03 1.70e+00
        pdb=" CG  PHE I 121 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE I 121 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE I 121 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE I 121 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE I 121 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE I 121 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 121 "    0.009 2.00e-02 2.50e+03   9.82e-03 1.69e+00
        pdb=" CG  PHE A 121 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 121 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 121 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 121 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 121 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 121 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 437 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.05: 1672
        3.05 -     3.51: 2324
        3.51 -     3.97: 4274
        3.97 -     4.44: 4652
        4.44 -     4.90: 9092
  Nonbonded interactions: 22014
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 130 "
            pdb=" NE2 GLN C 130 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" OE1 GLN B 130 "
            pdb=" NE2 GLN D 130 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" OE1 GLN E 130 "
            pdb=" NE2 GLN G 130 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" OE1 GLN G 130 "
            pdb=" NE2 GLN I 130 "
     model   vdw
     2.583 3.120
  nonbonded pdb=" OE1 GLN H 130 "
            pdb=" NE2 GLN J 130 "
     model   vdw
     2.583 3.120
  ... (remaining 22009 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 individual isotropic
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:             1.210
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.190
  Find NCS groups from input model:        0.020
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
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   0.067   2630  Z= 0.259
  Angle     :  1.252   9.205   3550  Z= 0.656
  Chirality :  0.053   0.131    440
  Planarity :  0.003   0.010    440
  Dihedral  : 18.134  75.257    930
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 41.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 30.00 %
    Favored  : 64.29 %
  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 are not related in a simple way.
  whole: -6.34 (0.31), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.83 (0.24), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G 115 
 PHE   0.022   0.003   PHE B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00606 /  0.26 ( 2630)
  covalent geometry    : angle       1.25187 /  0.66 ( 3550)
  hydrogen bonds       : bond        0.13419 /  8.25 (   24)
  hydrogen bonds       : angle       6.54856 /  4.10 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.5510 (ptpt) cc_final: 0.4822 (ptmm)
REVERT: A  128 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7111 (m-30)
REVERT: H  128 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6786 (m-30)
REVERT: J  109 LEU cc_start: 0.5799 (tp) cc_final: 0.5178 (pt)
  outliers start: 16
  outliers final: 13
  residues processed: 36
  average time/residue: 0.0211
  time to fit residues: 1.0985
Evaluate side-chains
  34 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 19
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  128 ASP
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  128 ASP
Chi-restraints excluded: chain I residue  112 VAL
Chi-restraints excluded: chain I residue  128 ASP
Chi-restraints excluded: chain J residue  112 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5740 r_free = 0.5740 target = 0.324074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5644 r_free = 0.5644 target = 0.272255 restraints weight = 3027.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.5592 rms_B_bonded: 2.79
r_work: 0.5607 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.5487 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.5487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2630  Z= 0.182
  Angle     :  0.867   6.851   3550  Z= 0.424
  Chirality :  0.046   0.133    440
  Planarity :  0.003   0.015    440
  Dihedral  :  7.094  25.554    350
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers : 13.57 %
    Allowed  : 19.29 %
    Favored  : 67.14 %
  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 are not related in a simple way.
  whole: -6.25 (0.30), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.76 (0.23), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 115 
 PHE   0.016   0.002   PHE E 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.18 ( 2630)
  covalent geometry    : angle       0.86744 /  0.42 ( 3550)
  hydrogen bonds       : bond        0.02754 /  1.80 (   24)
  hydrogen bonds       : angle       3.47467 /  2.28 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 18
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.5581 (ptpt) cc_final: 0.4862 (ptmm)
REVERT: A  120 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4807 (tp30)
REVERT: B  119 LYS cc_start: 0.6207 (ptpt) cc_final: 0.5264 (ptmt)
REVERT: D  120 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.4962 (mm-30)
REVERT: F  120 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.3811 (tp30)
REVERT: G  120 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.4954 (tp30)
REVERT: I  105 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4319 (tt)
REVERT: I  120 GLU cc_start: 0.4733 (OUTLIER) cc_final: 0.4483 (tp30)
REVERT: J  105 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.4036 (tt)
  outliers start: 38
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0392
  time to fit residues: 2.8333
Evaluate side-chains
  30 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 13
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  104 LEU
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  105 LEU
Chi-restraints excluded: chain I residue  120 GLU
Chi-restraints excluded: chain J residue  105 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.3788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5705 r_free = 0.5705 target = 0.322725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5615 r_free = 0.5615 target = 0.270134 restraints weight = 2974.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.5530 rms_B_bonded: 2.68
r_work: 0.5569 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.5446 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.5446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2630  Z= 0.156
  Angle     :  0.819   8.981   3550  Z= 0.394
  Chirality :  0.044   0.119    440
  Planarity :  0.003   0.011    440
  Dihedral  :  6.427  27.734    336
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers : 11.43 %
    Allowed  : 20.71 %
    Favored  : 67.86 %
  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 are not related in a simple way.
  whole: -6.08 (0.30), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.63 (0.23), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 115 
 PHE   0.011   0.002   PHE B 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 2630)
  covalent geometry    : angle       0.81921 /  0.39 ( 3550)
  hydrogen bonds       : bond        0.02319 /  1.44 (   24)
  hydrogen bonds       : angle       3.33498 /  2.14 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 23
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.5410 (ptpt) cc_final: 0.4681 (ptmm)
REVERT: B  119 LYS cc_start: 0.6009 (ptpt) cc_final: 0.4981 (ptmt)
REVERT: C  119 LYS cc_start: 0.5415 (ptpt) cc_final: 0.4268 (pttt)
REVERT: D  120 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5651 (tp30)
REVERT: E  119 LYS cc_start: 0.5540 (ptpt) cc_final: 0.4339 (pttt)
REVERT: F  120 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4131 (tp30)
REVERT: G  120 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5094 (tp30)
REVERT: J  122 THR cc_start: 0.5888 (OUTLIER) cc_final: 0.5670 (t)
  outliers start: 32
  outliers final: 17
  residues processed: 51
  average time/residue: 0.0610
  time to fit residues: 3.7849
Evaluate side-chains
  39 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 18
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain G residue  122 THR
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Chi-restraints excluded: chain J residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.0982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5730 r_free = 0.5730 target = 0.327553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5642 r_free = 0.5642 target = 0.274012 restraints weight = 2945.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.5573 rms_B_bonded: 2.66
r_work: 0.5622 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.5500 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.5500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2630  Z= 0.144
  Angle     :  0.761   7.076   3550  Z= 0.370
  Chirality :  0.044   0.119    440
  Planarity :  0.002   0.010    440
  Dihedral  :  6.124  26.168    334
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.55 %
    Favored  : 86.45 %
  Rotamer:
    Outliers : 10.36 %
    Allowed  : 21.43 %
    Favored  : 68.21 %
  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 are not related in a simple way.
  whole: -6.10 (0.30), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.65 (0.23), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG I 115 
 PHE   0.016   0.001   PHE J 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 2630)
  covalent geometry    : angle       0.76143 /  0.37 ( 3550)
  hydrogen bonds       : bond        0.01774 /  1.14 (   24)
  hydrogen bonds       : angle       3.27556 /  2.12 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 20
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.5326 (ptpt) cc_final: 0.4625 (ptmm)
REVERT: B  119 LYS cc_start: 0.5580 (ptpt) cc_final: 0.4553 (ptmt)
REVERT: B  120 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.4735 (tp30)
REVERT: C  110 VAL cc_start: 0.6436 (OUTLIER) cc_final: 0.6160 (t)
REVERT: C  119 LYS cc_start: 0.5211 (ptpt) cc_final: 0.4128 (pttt)
REVERT: D  119 LYS cc_start: 0.6143 (ptpt) cc_final: 0.4965 (ptmt)
REVERT: E  119 LYS cc_start: 0.5345 (ptpt) cc_final: 0.4216 (pttt)
REVERT: F  119 LYS cc_start: 0.5845 (ptpt) cc_final: 0.4953 (ptmt)
REVERT: F  120 GLU cc_start: 0.5035 (OUTLIER) cc_final: 0.4254 (tp30)
REVERT: G  110 VAL cc_start: 0.6593 (OUTLIER) cc_final: 0.6233 (t)
REVERT: G  120 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5361 (tp30)
REVERT: I  122 THR cc_start: 0.6199 (OUTLIER) cc_final: 0.5960 (t)
  outliers start: 29
  outliers final: 16
  residues processed: 45
  average time/residue: 0.0593
  time to fit residues: 3.2979
Evaluate side-chains
  42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 20
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain G residue  122 THR
Chi-restraints excluded: chain H residue  110 VAL
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    2.0784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5548 r_free = 0.5548 target = 0.248327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5239 r_free = 0.5239 target = 0.211304 restraints weight = 2809.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.5301 rms_B_bonded: 3.49
r_work: 0.5186 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.5186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.5728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2630  Z= 0.183
  Angle     :  0.876  10.355   3550  Z= 0.414
  Chirality :  0.047   0.193    440
  Planarity :  0.003   0.010    440
  Dihedral  :  6.788  33.286    334
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.77 %
    Favored  : 83.23 %
  Rotamer:
    Outliers : 10.71 %
    Allowed  : 23.93 %
    Favored  : 65.36 %
  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 are not related in a simple way.
  whole: -6.24 (0.28), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.75 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 115 
 PHE   0.013   0.002   PHE B 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.18 ( 2630)
  covalent geometry    : angle       0.87582 /  0.41 ( 3550)
  hydrogen bonds       : bond        0.02448 /  1.51 (   24)
  hydrogen bonds       : angle       4.06014 /  2.65 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 21
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.4645 (mtt90) cc_final: 0.2337 (pmt-80)
REVERT: A  119 LYS cc_start: 0.5140 (ptpt) cc_final: 0.4412 (ptmm)
REVERT: B  119 LYS cc_start: 0.5015 (ptpt) cc_final: 0.3983 (ptmt)
REVERT: B  120 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.4630 (tp30)
REVERT: C  119 LYS cc_start: 0.5039 (ptpt) cc_final: 0.3879 (pttt)
REVERT: E  119 LYS cc_start: 0.5046 (ptpt) cc_final: 0.3877 (pttt)
REVERT: F  120 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3290 (tp30)
REVERT: G  120 GLU cc_start: 0.4859 (OUTLIER) cc_final: 0.4327 (tp30)
REVERT: I  122 THR cc_start: 0.6701 (OUTLIER) cc_final: 0.6496 (t)
  outliers start: 30
  outliers final: 16
  residues processed: 47
  average time/residue: 0.0662
  time to fit residues: 3.7780
Evaluate side-chains
  41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 21
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.5382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.321890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5547 r_free = 0.5547 target = 0.259046 restraints weight = 2934.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.5485 rms_B_bonded: 2.60
r_work: 0.5525 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.5402 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.5402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.6004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   2630  Z= 0.157
  Angle     :  0.840   9.014   3550  Z= 0.391
  Chirality :  0.046   0.178    440
  Planarity :  0.002   0.011    440
  Dihedral  :  6.398  29.128    334
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.84 %
    Favored  : 85.16 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 25.71 %
    Favored  : 64.29 %
  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 are not related in a simple way.
  whole: -6.29 (0.29), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.79 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 115 
 PHE   0.012   0.001   PHE B 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 2630)
  covalent geometry    : angle       0.83972 /  0.39 ( 3550)
  hydrogen bonds       : bond        0.01864 /  1.17 (   24)
  hydrogen bonds       : angle       3.66771 /  2.40 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 24
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.4979 (mtt90) cc_final: 0.2816 (pmt-80)
REVERT: A  119 LYS cc_start: 0.5648 (ptpt) cc_final: 0.4938 (ptmm)
REVERT: B  119 LYS cc_start: 0.5444 (ptpt) cc_final: 0.4344 (pttp)
REVERT: B  120 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5388 (tp30)
REVERT: C  110 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6504 (t)
REVERT: C  119 LYS cc_start: 0.5438 (ptpt) cc_final: 0.4380 (pttt)
REVERT: D  120 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4822 (tp30)
REVERT: F  120 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4327 (tp30)
REVERT: G  120 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5184 (tp30)
REVERT: I  122 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6469 (t)
REVERT: J  119 LYS cc_start: 0.5722 (ptpt) cc_final: 0.4928 (mmmt)
  outliers start: 28
  outliers final: 16
  residues processed: 48
  average time/residue: 0.0686
  time to fit residues: 3.9588
Evaluate side-chains
  42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 20
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.6184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5677 r_free = 0.5677 target = 0.319107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5566 r_free = 0.5566 target = 0.261669 restraints weight = 2890.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.5471 rms_B_bonded: 2.66
r_work: 0.5540 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.5417 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.5417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.6251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2630  Z= 0.162
  Angle     :  0.817   9.612   3550  Z= 0.387
  Chirality :  0.046   0.150    440
  Planarity :  0.002   0.011    440
  Dihedral  :  6.324  28.384    334
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.77 %
    Favored  : 83.23 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 29.64 %
    Favored  : 63.21 %
  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 are not related in a simple way.
  whole: -6.30 (0.28), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.79 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 115 
 PHE   0.012   0.001   PHE B 117 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.16 ( 2630)
  covalent geometry    : angle       0.81731 /  0.39 ( 3550)
  hydrogen bonds       : bond        0.01943 /  1.21 (   24)
  hydrogen bonds       : angle       3.77784 /  2.46 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 24
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.4797 (mtt90) cc_final: 0.2584 (pmt-80)
REVERT: A  119 LYS cc_start: 0.5852 (ptpt) cc_final: 0.5054 (ptmm)
REVERT: B  119 LYS cc_start: 0.5316 (ptpt) cc_final: 0.4283 (pttp)
REVERT: B  120 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5574 (tp30)
REVERT: C  119 LYS cc_start: 0.5370 (ptpt) cc_final: 0.4335 (pttt)
REVERT: D  122 THR cc_start: 0.6948 (OUTLIER) cc_final: 0.6724 (t)
REVERT: E  105 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5552 (tt)
REVERT: G  119 LYS cc_start: 0.5778 (ptpt) cc_final: 0.4717 (pttp)
REVERT: I  122 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.6478 (t)
REVERT: J  119 LYS cc_start: 0.5719 (ptpt) cc_final: 0.4867 (mmmt)
  outliers start: 20
  outliers final: 14
  residues processed: 40
  average time/residue: 0.0883
  time to fit residues: 4.1108
Evaluate side-chains
  41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 23
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  112 VAL
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 10 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0170
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5136

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5905 r_free = 0.5905 target = 0.353496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5780 r_free = 0.5780 target = 0.289624 restraints weight = 2813.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.5598 rms_B_bonded: 3.21
r_work: 0.5349 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.5349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.6515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2630  Z= 0.119
  Angle     :  0.688   6.478   3550  Z= 0.336
  Chirality :  0.045   0.148    440
  Planarity :  0.002   0.009    440
  Dihedral  :  5.338  20.870    333
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  7.86 %
    Allowed  : 28.93 %
    Favored  : 63.21 %
  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 are not related in a simple way.
  whole: -6.15 (0.29), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.68 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 115 
 PHE   0.013   0.001   PHE I 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 2630)
  covalent geometry    : angle       0.68839 /  0.34 ( 3550)
  hydrogen bonds       : bond        0.01295 /  0.73 (   24)
  hydrogen bonds       : angle       2.78913 /  1.79 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 26
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B  120 GLU cc_start: 0.5259 (OUTLIER) cc_final: 0.4931 (tp30)
REVERT: C  110 VAL cc_start: 0.6378 (OUTLIER) cc_final: 0.6103 (t)
REVERT: C  119 LYS cc_start: 0.4915 (ptpt) cc_final: 0.3943 (pttt)
REVERT: D  120 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.4625 (tp30)
REVERT: F  119 LYS cc_start: 0.4975 (ptpt) cc_final: 0.4078 (pttp)
REVERT: F  120 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4090 (tp30)
REVERT: G  110 VAL cc_start: 0.6660 (OUTLIER) cc_final: 0.6332 (t)
REVERT: G  120 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4782 (tp30)
REVERT: I  122 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.6050 (t)
  outliers start: 22
  outliers final: 8
  residues processed: 45
  average time/residue: 0.0574
  time to fit residues: 3.1963
Evaluate side-chains
  36 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 21
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   overall best weight:    2.5988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5668 r_free = 0.5668 target = 0.313641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5555 r_free = 0.5555 target = 0.255738 restraints weight = 2949.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.5442 rms_B_bonded: 2.64
r_work: 0.5517 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.5397 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.5397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.6638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   2630  Z= 0.201
  Angle     :  0.882   9.436   3550  Z= 0.420
  Chirality :  0.051   0.257    440
  Planarity :  0.003   0.010    440
  Dihedral  :  6.171  25.869    331
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 18.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.35 %
    Favored  : 80.65 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 30.00 %
    Favored  : 63.21 %
  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 are not related in a simple way.
  whole: -6.28 (0.28), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.78 (0.21), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 115 
 PHE   0.016   0.002   PHE I 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.20 ( 2630)
  covalent geometry    : angle       0.88206 /  0.42 ( 3550)
  hydrogen bonds       : bond        0.02402 /  1.45 (   24)
  hydrogen bonds       : angle       4.33663 /  2.83 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 22
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.4736 (mtt90) cc_final: 0.2535 (pmt-80)
REVERT: A  119 LYS cc_start: 0.6141 (ptpt) cc_final: 0.5282 (ptmm)
REVERT: B  119 LYS cc_start: 0.5514 (ptpt) cc_final: 0.4458 (pttp)
REVERT: B  120 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5333 (tp30)
REVERT: C  119 LYS cc_start: 0.5665 (ptpt) cc_final: 0.4624 (pttt)
REVERT: D  105 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5193 (tt)
REVERT: D  120 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5129 (tp30)
REVERT: F  120 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4638 (tp30)
REVERT: G  120 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5434 (tp30)
REVERT: I  122 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6450 (t)
REVERT: J  119 LYS cc_start: 0.5710 (ptpt) cc_final: 0.4909 (mmmt)
  outliers start: 19
  outliers final: 12
  residues processed: 41
  average time/residue: 0.0862
  time to fit residues: 4.0635
Evaluate side-chains
  38 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 20
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  112 VAL
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5750 r_free = 0.5750 target = 0.325054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5648 r_free = 0.5648 target = 0.266289 restraints weight = 2944.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.5536 rms_B_bonded: 2.72
r_work: 0.5605 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.5489 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.5489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.6705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2630  Z= 0.147
  Angle     :  0.778   8.577   3550  Z= 0.375
  Chirality :  0.047   0.227    440
  Planarity :  0.002   0.011    440
  Dihedral  :  5.773  20.079    331
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 30.71 %
    Favored  : 62.86 %
  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 are not related in a simple way.
  whole: -6.19 (0.29), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.71 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 115 
 PHE   0.018   0.001   PHE I 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 2630)
  covalent geometry    : angle       0.77782 /  0.37 ( 3550)
  hydrogen bonds       : bond        0.01622 /  1.02 (   24)
  hydrogen bonds       : angle       3.50480 /  2.29 (   72)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 22
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A  115 ARG cc_start: 0.4649 (mtt90) cc_final: 0.2507 (pmt-80)
REVERT: A  119 LYS cc_start: 0.5668 (ptpt) cc_final: 0.4913 (ptmm)
REVERT: B  119 LYS cc_start: 0.5141 (ptpt) cc_final: 0.4124 (pttp)
REVERT: B  120 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5294 (tp30)
REVERT: C  110 VAL cc_start: 0.6574 (OUTLIER) cc_final: 0.6248 (t)
REVERT: C  119 LYS cc_start: 0.5483 (ptpt) cc_final: 0.4516 (pttt)
REVERT: D  120 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5118 (tp30)
REVERT: F  119 LYS cc_start: 0.5568 (ptpt) cc_final: 0.4759 (pttp)
REVERT: F  120 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.4908 (tp30)
REVERT: G  120 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5559 (tp30)
REVERT: I  122 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6222 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 38
  average time/residue: 0.0676
  time to fit residues: 3.0169
Evaluate side-chains
  38 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 22
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain C residue  110 VAL
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain D residue  120 GLU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  110 VAL
Chi-restraints excluded: chain E residue  112 VAL
Chi-restraints excluded: chain E residue  122 THR
Chi-restraints excluded: chain E residue  128 ASP
Chi-restraints excluded: chain F residue  120 GLU
Chi-restraints excluded: chain G residue  110 VAL
Chi-restraints excluded: chain G residue  120 GLU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain I residue  104 LEU
Chi-restraints excluded: chain I residue  122 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0060
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.6600

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5784 r_free = 0.5784 target = 0.327178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5652 r_free = 0.5652 target = 0.272382 restraints weight = 2801.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.5501 rms_B_bonded: 3.56
r_work: 0.5268 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.5268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.6844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2630  Z= 0.127
  Angle     :  0.717   8.600   3550  Z= 0.345
  Chirality :  0.046   0.222    440
  Planarity :  0.002   0.009    440
  Dihedral  :  5.173  16.675    331
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 31.79 %
    Favored  : 63.21 %
  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 are not related in a simple way.
  whole: -6.01 (0.29), residues: 310
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.57 (0.22), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 115 
 PHE   0.019   0.001   PHE I 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 2630)
  covalent geometry    : angle       0.71683 /  0.34 ( 3550)
  hydrogen bonds       : bond        0.01360 /  0.83 (   24)
  hydrogen bonds       : angle       3.05825 /  1.96 (   72)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 797.96 seconds
wall clock time: 14 minutes 20.94 seconds (860.94 seconds total)