Starting phenix.real_space_refine
on Fri Aug 22 12:39:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kew_37170/08_2025/8kew_37170.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C     978      2.51       5
     N     252      2.21       5
     O     264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1500
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
  Restraints were copied for chains:
    G, A, C, B, D
  Time building chain proxies: 0.61, per 1000 atoms: 0.41
  Number of scatterers: 1500
  At special positions: 0
  Unit cell: (68.89, 68.89, 36.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     264      8.00
     N     252      7.00
     C     978      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 80.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  336

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 29.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 12 through 13
      removed outlier: 6.392A  pdb=" N   VAL F  12 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL A  12 " --> pdb=" O   HIS B  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 16 through 17
    Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 25
      removed outlier: 6.397A  pdb=" N   VAL F  24 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A  24 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 30 through 36
      removed outlier: 6.909A  pdb=" N   ILE A  31 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE F  32 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLY A  33 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE B  31 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE A  32 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLY B  33 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 40 through 41
    Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13
      removed outlier: 6.413A  pdb=" N   VAL G  12 " --> pdb=" O   HIS C  13 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   VAL C  12 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 17
    Processing sheet with id=AA8, first strand: chain 'G' and resid 24 through 25
      removed outlier: 6.410A  pdb=" N   VAL G  24 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL C  24 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 30 through 36
      removed outlier: 6.914A  pdb=" N   ILE C  31 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ILE G  32 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLY C  33 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ILE D  31 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE C  32 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLY D  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 40 through 41

    20 hydrogen bonds defined for protein.
    60 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: 0.17

  Time building geometry restraints manager: 0.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 486
        1.34 -     1.45: 181
        1.45 -     1.56: 845
        1.56 -     1.68: 0
        1.68 -     1.79: 12
  Bond restraints: 1524
  Sorted by residual:
  bond pdb=" CG  LEU F  34 "
       pdb=" CD1 LEU F  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  bond pdb=" CG  LEU G  34 "
       pdb=" CD1 LEU G  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  bond pdb=" CG  LEU B  34 "
       pdb=" CD1 LEU B  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.62e+00
  bond pdb=" CG  LEU A  34 "
       pdb=" CD1 LEU A  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  bond pdb=" CG  LEU C  34 "
       pdb=" CD1 LEU C  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  ... (remaining 1519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 1617
        0.88 -     1.75: 313
        1.75 -     2.63: 80
        2.63 -     3.50: 30
        3.50 -     4.38: 6
  Bond angle restraints: 2046
  Sorted by residual:
  angle pdb=" N   GLU C  22 "
        pdb=" CA  GLU C  22 "
        pdb=" C   GLU C  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.83   -4.38 1.26e+00 6.30e-01 1.21e+01
  angle pdb=" N   GLU F  22 "
        pdb=" CA  GLU F  22 "
        pdb=" C   GLU F  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLU A  22 "
        pdb=" CA  GLU A  22 "
        pdb=" C   GLU A  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.19e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.79   -4.34 1.26e+00 6.30e-01 1.19e+01
  ... (remaining 2041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    12.24: 708
       12.24 -    24.48: 96
       24.48 -    36.71: 24
       36.71 -    48.95: 12
       48.95 -    61.18: 6
  Dihedral angle restraints: 846
    sinusoidal: 306
      harmonic: 540
  Sorted by residual:
  dihedral pdb=" CA  HIS F  14 "
           pdb=" C   HIS F  14 "
           pdb=" N   GLN F  15 "
           pdb=" CA  GLN F  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.19   12.81     0      5.00e+00 4.00e-02 6.56e+00
  dihedral pdb=" CA  HIS D  14 "
           pdb=" C   HIS D  14 "
           pdb=" N   GLN D  15 "
           pdb=" CA  GLN D  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.21   12.79     0      5.00e+00 4.00e-02 6.55e+00
  dihedral pdb=" CA  HIS G  14 "
           pdb=" C   HIS G  14 "
           pdb=" N   GLN G  15 "
           pdb=" CA  GLN G  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.21   12.79     0      5.00e+00 4.00e-02 6.54e+00
  ... (remaining 843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 79
       0.029 -    0.058: 53
       0.058 -    0.087: 42
       0.087 -    0.116: 24
       0.116 -    0.145: 36
  Chirality restraints: 234
  Sorted by residual:
  chirality pdb=" CA  VAL F  39 "
            pdb=" N   VAL F  39 "
            pdb=" C   VAL F  39 "
            pdb=" CB  VAL F  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  VAL C  39 "
            pdb=" N   VAL C  39 "
            pdb=" C   VAL C  39 "
            pdb=" CB  VAL C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  VAL D  39 "
            pdb=" N   VAL D  39 "
            pdb=" C   VAL D  39 "
            pdb=" CB  VAL D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 231 not shown)

  Planarity restraints: 258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  20 "    0.006 2.00e-02 2.50e+03   4.74e-03 3.94e-01
        pdb=" CG  PHE A  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  20 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  20 "    0.006 2.00e-02 2.50e+03   4.71e-03 3.88e-01
        pdb=" CG  PHE G  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  20 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  20 "    0.006 2.00e-02 2.50e+03   4.67e-03 3.82e-01
        pdb=" CG  PHE D  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  20 "    0.001 2.00e-02 2.50e+03
  ... (remaining 255 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 585
        2.89 -     3.39: 1237
        3.39 -     3.89: 2379
        3.89 -     4.40: 2364
        4.40 -     4.90: 4769
  Nonbonded interactions: 11334
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  27 "
            pdb=" N   LYS B  28 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OD1 ASN C  27 "
            pdb=" N   LYS C  28 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OD1 ASN D  27 "
            pdb=" N   LYS D  28 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" OD1 ASN G  27 "
            pdb=" N   LYS G  28 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" OD1 ASN F  27 "
            pdb=" N   LYS F  28 "
     model   vdw
     2.388 3.120
  ... (remaining 11329 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 'F'
  selection = chain 'G'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.160
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
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      :  0.010   0.045   1524  Z= 0.408
  Angle     :  0.841   4.375   2046  Z= 0.523
  Chirality :  0.070   0.145    234
  Planarity :  0.003   0.006    258
  Dihedral  : 14.456  61.184    510
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.87 (0.44), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.34), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR A  10 
 PHE   0.011   0.002   PHE A  20 
 HIS   0.005   0.002   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00958 ( 1524)
  covalent geometry    : angle       0.84085 ( 2046)
  hydrogen bonds       : bond        0.12557 (   20)
  hydrogen bonds       : angle       7.08663 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.062 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8178 (mm-30) cc_final: 0.6816 (pt0)
REVERT: F   26 SER cc_start: 0.8743 (m) cc_final: 0.8178 (t)
REVERT: G   22 GLU cc_start: 0.8267 (mm-30) cc_final: 0.6727 (pt0)
REVERT: G   26 SER cc_start: 0.8773 (m) cc_final: 0.8178 (t)
REVERT: A   10 TYR cc_start: 0.7392 (m-80) cc_final: 0.7077 (m-80)
REVERT: A   26 SER cc_start: 0.8559 (m) cc_final: 0.8005 (t)
REVERT: A   27 ASN cc_start: 0.8853 (t0) cc_final: 0.8608 (t0)
REVERT: C   22 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7965 (mm-30)
REVERT: C   26 SER cc_start: 0.8652 (m) cc_final: 0.7983 (t)
REVERT: B   26 SER cc_start: 0.8779 (m) cc_final: 0.8287 (t)
REVERT: D   14 HIS cc_start: 0.8287 (m90) cc_final: 0.7996 (m90)
REVERT: D   26 SER cc_start: 0.8757 (m) cc_final: 0.8231 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0786
  time to fit residues: 2.8077
Evaluate side-chains
  25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0270
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.9240

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.119609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.090198 restraints weight = 1727.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 3.25
r_work: 0.3152 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1524  Z= 0.098
  Angle     :  0.465   2.306   2046  Z= 0.274
  Chirality :  0.062   0.131    234
  Planarity :  0.001   0.006    258
  Dihedral  :  4.732  11.063    204
  Min Nonbonded Distance : 2.673

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.09 (0.47), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.36), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.004   0.001   PHE B  20 
 HIS   0.002   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 1524)
  covalent geometry    : angle       0.46485 ( 2046)
  hydrogen bonds       : bond        0.01472 (   20)
  hydrogen bonds       : angle       4.32762 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.058 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8350 (mm-30) cc_final: 0.6791 (pt0)
REVERT: F   26 SER cc_start: 0.8262 (m) cc_final: 0.7747 (t)
REVERT: G   22 GLU cc_start: 0.8346 (mm-30) cc_final: 0.6708 (pt0)
REVERT: G   26 SER cc_start: 0.8296 (m) cc_final: 0.7800 (t)
REVERT: A   10 TYR cc_start: 0.7442 (m-80) cc_final: 0.7124 (m-80)
REVERT: A   14 HIS cc_start: 0.8050 (m90) cc_final: 0.7624 (m90)
REVERT: A   26 SER cc_start: 0.7820 (m) cc_final: 0.7327 (t)
REVERT: C   22 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7737 (mm-30)
REVERT: C   26 SER cc_start: 0.7978 (m) cc_final: 0.7427 (t)
REVERT: B   26 SER cc_start: 0.8185 (m) cc_final: 0.7692 (t)
REVERT: D   14 HIS cc_start: 0.8214 (m90) cc_final: 0.7911 (m90)
REVERT: D   26 SER cc_start: 0.8166 (m) cc_final: 0.7656 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0395
  time to fit residues: 1.4163
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0170
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.120152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.093273 restraints weight = 1764.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 3.20
r_work: 0.3308 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1524  Z= 0.068
  Angle     :  0.413   1.989   2046  Z= 0.243
  Chirality :  0.060   0.131    234
  Planarity :  0.001   0.005    258
  Dihedral  :  4.267  10.144    204
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  9.33 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.49), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.38), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.002   0.001   PHE A  20 
 HIS   0.001   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 ( 1524)
  covalent geometry    : angle       0.41293 ( 2046)
  hydrogen bonds       : bond        0.01273 (   20)
  hydrogen bonds       : angle       3.88253 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.059 
Fit side-chains
REVERT: F   14 HIS cc_start: 0.8359 (m90) cc_final: 0.8130 (m90)
REVERT: F   22 GLU cc_start: 0.8285 (mm-30) cc_final: 0.6794 (pt0)
REVERT: F   26 SER cc_start: 0.8270 (m) cc_final: 0.7746 (t)
REVERT: G   22 GLU cc_start: 0.8190 (mm-30) cc_final: 0.6762 (pt0)
REVERT: G   26 SER cc_start: 0.8257 (m) cc_final: 0.7746 (t)
REVERT: A   10 TYR cc_start: 0.7378 (m-80) cc_final: 0.7066 (m-80)
REVERT: A   14 HIS cc_start: 0.8038 (m90) cc_final: 0.7755 (m90)
REVERT: A   22 GLU cc_start: 0.8044 (tp30) cc_final: 0.7747 (mm-30)
REVERT: A   26 SER cc_start: 0.7830 (m) cc_final: 0.7283 (t)
REVERT: C   22 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7804 (mm-30)
REVERT: C   26 SER cc_start: 0.7932 (m) cc_final: 0.7425 (t)
REVERT: B   26 SER cc_start: 0.8088 (m) cc_final: 0.7540 (t)
REVERT: D   14 HIS cc_start: 0.8187 (m90) cc_final: 0.7965 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0362
  time to fit residues: 1.3766
Evaluate side-chains
  30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0040
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0270
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5654

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.119020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.091874 restraints weight = 1750.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 3.27
r_work: 0.3314 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1524  Z= 0.073
  Angle     :  0.422   3.847   2046  Z= 0.246
  Chirality :  0.060   0.125    234
  Planarity :  0.001   0.003    258
  Dihedral  :  4.064   9.739    204
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 12.00 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.26 (0.50), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.38), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR A  10 
 PHE   0.003   0.001   PHE G  20 
 HIS   0.001   0.000   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 1524)
  covalent geometry    : angle       0.42198 ( 2046)
  hydrogen bonds       : bond        0.01168 (   20)
  hydrogen bonds       : angle       3.90101 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.059 
Fit side-chains
REVERT: F   26 SER cc_start: 0.8187 (m) cc_final: 0.7692 (t)
REVERT: G   14 HIS cc_start: 0.8282 (m90) cc_final: 0.8053 (m90)
REVERT: G   16 LYS cc_start: 0.8254 (tttt) cc_final: 0.8043 (tttm)
REVERT: G   26 SER cc_start: 0.8175 (m) cc_final: 0.7636 (t)
REVERT: A   10 TYR cc_start: 0.7322 (m-80) cc_final: 0.6981 (m-80)
REVERT: A   14 HIS cc_start: 0.8018 (m90) cc_final: 0.7789 (m90)
REVERT: A   22 GLU cc_start: 0.8013 (tp30) cc_final: 0.7692 (mm-30)
REVERT: A   26 SER cc_start: 0.7820 (m) cc_final: 0.7270 (t)
REVERT: C   22 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: C   26 SER cc_start: 0.7794 (m) cc_final: 0.7274 (t)
REVERT: B   26 SER cc_start: 0.7963 (m) cc_final: 0.7447 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0440
  time to fit residues: 1.5955
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.112983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.086793 restraints weight = 1968.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.45
r_work: 0.3271 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   1524  Z= 0.086
  Angle     :  0.434   3.844   2046  Z= 0.254
  Chirality :  0.060   0.126    234
  Planarity :  0.001   0.003    258
  Dihedral  :  3.964   9.847    204
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.00 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.53), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.003   0.001   PHE G  20 
 HIS   0.001   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 1524)
  covalent geometry    : angle       0.43410 ( 2046)
  hydrogen bonds       : bond        0.00934 (   20)
  hydrogen bonds       : angle       4.08410 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.054 
Fit side-chains
REVERT: F   26 SER cc_start: 0.8219 (m) cc_final: 0.7726 (t)
REVERT: G   14 HIS cc_start: 0.8274 (m90) cc_final: 0.8071 (m90)
REVERT: G   16 LYS cc_start: 0.8271 (tttt) cc_final: 0.8040 (tttm)
REVERT: G   26 SER cc_start: 0.8175 (m) cc_final: 0.7660 (t)
REVERT: A   10 TYR cc_start: 0.7345 (m-80) cc_final: 0.7050 (m-80)
REVERT: A   22 GLU cc_start: 0.8080 (tp30) cc_final: 0.7796 (mm-30)
REVERT: A   26 SER cc_start: 0.7851 (m) cc_final: 0.7302 (t)
REVERT: C   22 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7866 (mm-30)
REVERT: C   26 SER cc_start: 0.7776 (m) cc_final: 0.7261 (t)
REVERT: B   26 SER cc_start: 0.8021 (m) cc_final: 0.7448 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0444
  time to fit residues: 1.5510
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 13 optimal weight:    0.2980
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.2586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.115365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.086256 restraints weight = 1759.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 3.26
r_work: 0.3238 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   1524  Z= 0.195
  Angle     :  0.529   2.721   2046  Z= 0.310
  Chirality :  0.063   0.138    234
  Planarity :  0.002   0.006    258
  Dihedral  :  4.725  10.757    204
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.61 (0.53), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.013   0.002   PHE G  20 
 HIS   0.003   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 1524)
  covalent geometry    : angle       0.52860 ( 2046)
  hydrogen bonds       : bond        0.01001 (   20)
  hydrogen bonds       : angle       4.05544 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.056 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8241 (mm-30) cc_final: 0.6785 (pt0)
REVERT: F   26 SER cc_start: 0.8299 (m) cc_final: 0.7813 (t)
REVERT: G   26 SER cc_start: 0.8182 (m) cc_final: 0.7717 (t)
REVERT: A   10 TYR cc_start: 0.7511 (m-80) cc_final: 0.7260 (m-80)
REVERT: A   22 GLU cc_start: 0.8187 (tp30) cc_final: 0.7873 (mm-30)
REVERT: A   26 SER cc_start: 0.7945 (m) cc_final: 0.7420 (t)
REVERT: C   22 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7687 (mm-30)
REVERT: C   26 SER cc_start: 0.7864 (m) cc_final: 0.7360 (t)
REVERT: B   26 SER cc_start: 0.8170 (m) cc_final: 0.7637 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0311
  time to fit residues: 1.1612
Evaluate side-chains
  27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.127423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.097349 restraints weight = 1731.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 3.39
r_work: 0.3365 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1524  Z= 0.142
  Angle     :  0.479   2.440   2046  Z= 0.282
  Chirality :  0.062   0.136    234
  Planarity :  0.001   0.004    258
  Dihedral  :  4.499  11.093    204
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 18.00 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.26 (0.55), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.95 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.008   0.001   PHE G  20 
 HIS   0.002   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 1524)
  covalent geometry    : angle       0.47933 ( 2046)
  hydrogen bonds       : bond        0.00939 (   20)
  hydrogen bonds       : angle       3.96010 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.058 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8213 (mm-30) cc_final: 0.6774 (pt0)
REVERT: F   26 SER cc_start: 0.8266 (m) cc_final: 0.7696 (t)
REVERT: G   26 SER cc_start: 0.8238 (m) cc_final: 0.7757 (t)
REVERT: A   10 TYR cc_start: 0.7389 (m-80) cc_final: 0.7146 (m-80)
REVERT: A   22 GLU cc_start: 0.8114 (tp30) cc_final: 0.7667 (mm-30)
REVERT: A   26 SER cc_start: 0.7868 (m) cc_final: 0.7265 (t)
REVERT: C   22 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7702 (mm-30)
REVERT: C   26 SER cc_start: 0.7817 (m) cc_final: 0.7237 (t)
REVERT: B   22 GLU cc_start: 0.8084 (tp30) cc_final: 0.7466 (mm-30)
REVERT: B   26 SER cc_start: 0.8072 (m) cc_final: 0.7522 (t)
REVERT: D   22 GLU cc_start: 0.8034 (tp30) cc_final: 0.7731 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0391
  time to fit residues: 1.3972
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   26 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.112465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.085968 restraints weight = 2018.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.50
r_work: 0.3275 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1524  Z= 0.092
  Angle     :  0.429   2.292   2046  Z= 0.252
  Chirality :  0.061   0.137    234
  Planarity :  0.001   0.003    258
  Dihedral  :  4.136  11.732    204
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 18.67 %
    Favored  : 80.67 %
  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: -1.08 (0.56), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.81 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.004   0.001   PHE G  20 
 HIS   0.002   0.000   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 1524)
  covalent geometry    : angle       0.42883 ( 2046)
  hydrogen bonds       : bond        0.00872 (   20)
  hydrogen bonds       : angle       4.01041 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.058 
Fit side-chains
REVERT: F   26 SER cc_start: 0.8169 (m) cc_final: 0.7643 (t)
REVERT: G   26 SER cc_start: 0.8276 (m) cc_final: 0.7813 (t)
REVERT: A   10 TYR cc_start: 0.7440 (m-80) cc_final: 0.7166 (m-80)
REVERT: A   22 GLU cc_start: 0.8100 (tp30) cc_final: 0.7752 (mm-30)
REVERT: C   22 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7754 (mm-30)
REVERT: C   26 SER cc_start: 0.7737 (m) cc_final: 0.7151 (t)
REVERT: B   26 SER cc_start: 0.8065 (m) cc_final: 0.7482 (t)
REVERT: D   22 GLU cc_start: 0.7970 (tp30) cc_final: 0.7701 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0308
  time to fit residues: 1.0881
Evaluate side-chains
  27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   26 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.118953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.089305 restraints weight = 1711.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.30
r_work: 0.3369 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   1524  Z= 0.153
  Angle     :  0.494   3.529   2046  Z= 0.291
  Chirality :  0.063   0.147    234
  Planarity :  0.002   0.014    258
  Dihedral  :  4.484  12.218    204
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.68 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR F  10 
 PHE   0.009   0.001   PHE G  20 
 HIS   0.002   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 1524)
  covalent geometry    : angle       0.49372 ( 2046)
  hydrogen bonds       : bond        0.00811 (   20)
  hydrogen bonds       : angle       3.84061 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.059 
Fit side-chains
REVERT: F   26 SER cc_start: 0.8191 (m) cc_final: 0.7638 (t)
REVERT: A   10 TYR cc_start: 0.7396 (m-80) cc_final: 0.7131 (m-80)
REVERT: A   22 GLU cc_start: 0.8138 (tp30) cc_final: 0.7747 (mm-30)
REVERT: C   22 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7770 (mm-30)
REVERT: C   26 SER cc_start: 0.7819 (m) cc_final: 0.7214 (t)
REVERT: B   26 SER cc_start: 0.8100 (m) cc_final: 0.7532 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0326
  time to fit residues: 1.0206
Evaluate side-chains
  23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.105330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.077682 restraints weight = 1941.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.48
r_work: 0.3314 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   1524  Z= 0.222
  Angle     :  0.578   4.309   2046  Z= 0.337
  Chirality :  0.065   0.157    234
  Planarity :  0.002   0.006    258
  Dihedral  :  5.110  12.646    204
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.71 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR G  10 
 PHE   0.014   0.002   PHE B  20 
 HIS   0.003   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 1524)
  covalent geometry    : angle       0.57777 ( 2046)
  hydrogen bonds       : bond        0.00916 (   20)
  hydrogen bonds       : angle       3.87438 (   60)

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.047 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8367 (mm-30) cc_final: 0.6866 (pt0)
REVERT: F   26 SER cc_start: 0.8314 (m) cc_final: 0.7771 (t)
REVERT: A   10 TYR cc_start: 0.7414 (m-80) cc_final: 0.7145 (m-80)
REVERT: C   26 SER cc_start: 0.7961 (m) cc_final: 0.7351 (t)
REVERT: B   26 SER cc_start: 0.8264 (m) cc_final: 0.7726 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0386
  time to fit residues: 1.3099
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.122609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.092438 restraints weight = 1672.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 3.30
r_work: 0.3230 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1524  Z= 0.119
  Angle     :  0.483   3.416   2046  Z= 0.284
  Chirality :  0.062   0.159    234
  Planarity :  0.001   0.003    258
  Dihedral  :  4.468  13.685    204
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 20.67 %
    Favored  : 78.67 %
  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: -0.86 (0.59), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.64 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR D  10 
 PHE   0.004   0.001   PHE C  20 
 HIS   0.002   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 1524)
  covalent geometry    : angle       0.48292 ( 2046)
  hydrogen bonds       : bond        0.00880 (   20)
  hydrogen bonds       : angle       3.90374 (   60)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 675.44 seconds
wall clock time: 12 minutes 48.38 seconds (768.38 seconds total)