Starting phenix.real_space_refine
on Fri Aug 22 16:05:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ff2_29036/08_2025/8ff2_29036.map"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1840      2.51       5
     N     510      2.21       5
     O     550      1.98       5
     H    2740      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5650
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 565
          Classifications: {'peptide': 38}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 37}
  Restraints were copied for chains:
    B, C, D, E, F, G, I, J, K
  Time building chain proxies: 0.63, per 1000 atoms: 0.11
  Number of scatterers: 5650
  At special positions: 0
  Unit cell: (70.56, 90.72, 47.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     550      8.00
     N     510      7.00
     C    1840      6.00
     H    2740      1.00
    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: 0.44
  Conformation dependent library (CDL) restraints added in 128.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  640

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21
      removed outlier: 6.728A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN C  15 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL E  18 " --> pdb=" O   GLN C  15 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU C  17 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   PHE E  20 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE C  19 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN E  15 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL G  18 " --> pdb=" O   GLN E  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU E  17 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE G  20 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE E  19 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN G  15 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   VAL J  18 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   LEU G  17 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE J  20 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE G  19 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21
      removed outlier: 6.728A  pdb=" N   GLN B  15 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL D  18 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU B  17 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE D  20 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE B  19 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN D  15 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   VAL F  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU D  17 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE F  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE D  19 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN F  15 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL I  18 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU F  17 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE I  20 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE F  19 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN I  15 " --> pdb=" O   LYS K  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL K  18 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU I  17 " --> pdb=" O   VAL K  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE K  20 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE I  19 " --> pdb=" O   PHE K  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32

    16 hydrogen bonds defined for protein.
    48 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: 1.14

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2740
        1.03 -     1.22: 0
        1.22 -     1.42: 1360
        1.42 -     1.61: 1590
        1.61 -     1.80: 20
  Bond restraints: 5710
  Sorted by residual:
  bond pdb=" CA  HIS G   6 "
       pdb=" C   HIS G   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 8.17e-01
  bond pdb=" CA  HIS D   6 "
       pdb=" C   HIS D   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 8.09e-01
  bond pdb=" CA  HIS K   6 "
       pdb=" C   HIS K   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.98e-01
  bond pdb=" CA  HIS A   6 "
       pdb=" C   HIS A   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.70e-01
  bond pdb=" CA  HIS C   6 "
       pdb=" C   HIS C   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.51e-01
  ... (remaining 5705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.48: 7927
        0.48 -     0.96: 1769
        0.96 -     1.44: 446
        1.44 -     1.91: 51
        1.91 -     2.39: 27
  Bond angle restraints: 10220
  Sorted by residual:
  angle pdb=" N   GLY D   9 "
        pdb=" CA  GLY D   9 "
        pdb=" C   GLY D   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.63    1.94 1.37e+00 5.33e-01 2.00e+00
  angle pdb=" N   GLY B   9 "
        pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.64    1.93 1.37e+00 5.33e-01 1.98e+00
  angle pdb=" N   GLY J   9 "
        pdb=" CA  GLY J   9 "
        pdb=" C   GLY J   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.67    1.90 1.37e+00 5.33e-01 1.92e+00
  angle pdb=" N   GLY K   9 "
        pdb=" CA  GLY K   9 "
        pdb=" C   GLY K   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.68    1.89 1.37e+00 5.33e-01 1.90e+00
  angle pdb=" N   GLY I   9 "
        pdb=" CA  GLY I   9 "
        pdb=" C   GLY I   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.68    1.89 1.37e+00 5.33e-01 1.90e+00
  ... (remaining 10215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.32: 2300
       11.32 -    22.65: 200
       22.65 -    33.97: 30
       33.97 -    45.29: 60
       45.29 -    56.61: 60
  Dihedral angle restraints: 2650
    sinusoidal: 1350
      harmonic: 1300
  Sorted by residual:
  dihedral pdb=" CA  HIS K  13 "
           pdb=" C   HIS K  13 "
           pdb=" N   HIS K  14 "
           pdb=" CA  HIS K  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.80   20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  HIS I  13 "
           pdb=" C   HIS I  13 "
           pdb=" N   HIS I  14 "
           pdb=" CA  HIS I  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.80   20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  HIS A  13 "
           pdb=" C   HIS A  13 "
           pdb=" N   HIS A  14 "
           pdb=" CA  HIS A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.81   20.19     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 2647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 214
       0.023 -    0.046: 126
       0.046 -    0.069: 0
       0.069 -    0.092: 10
       0.092 -    0.115: 50
  Chirality restraints: 400
  Sorted by residual:
  chirality pdb=" CA  VAL E  18 "
            pdb=" N   VAL E  18 "
            pdb=" C   VAL E  18 "
            pdb=" CB  VAL E  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.28e-01
  chirality pdb=" CA  VAL D  18 "
            pdb=" N   VAL D  18 "
            pdb=" C   VAL D  18 "
            pdb=" CB  VAL D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  chirality pdb=" CA  VAL G  18 "
            pdb=" N   VAL G  18 "
            pdb=" C   VAL G  18 "
            pdb=" CB  VAL G  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 397 not shown)

  Planarity restraints: 900
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  13 "    0.004 2.00e-02 2.50e+03   3.40e-03 2.60e-01
        pdb=" CG  HIS A  13 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS A  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS A  13 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS A  13 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS K  13 "   -0.005 2.00e-02 2.50e+03   3.35e-03 2.52e-01
        pdb=" CG  HIS K  13 "    0.008 2.00e-02 2.50e+03
        pdb=" ND1 HIS K  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS K  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS K  13 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS K  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS K  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS K  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS K  13 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  13 "    0.004 2.00e-02 2.50e+03   3.28e-03 2.43e-01
        pdb=" CG  HIS G  13 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  13 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS G  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS G  13 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS G  13 "    0.001 2.00e-02 2.50e+03
  ... (remaining 897 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.37: 2123
        2.37 -     2.93: 12418
        2.93 -     3.49: 13179
        3.49 -     4.04: 20019
        4.04 -     4.60: 28533
  Nonbonded interactions: 76272
  Sorted by model distance:
  nonbonded pdb="HE22 GLN A  15 "
            pdb=" O   VAL D  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN E  15 "
            pdb=" O   VAL I  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN B  15 "
            pdb=" O   VAL E  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN G  15 "
            pdb=" O   VAL K  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN F  15 "
            pdb=" O   VAL J  36 "
     model   vdw
     1.818 2.450
  ... (remaining 76267 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 'I'
  selection = chain 'J'
  selection = chain 'K'
}

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:             8.080
  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:             0.040
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.620
  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:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
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      :  0.005   0.017   2970  Z= 0.208
  Angle     :  0.429   1.979   3970  Z= 0.265
  Chirality :  0.044   0.115    400
  Planarity :  0.002   0.009    530
  Dihedral  : 10.635  42.562   1020
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.01 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B   5 
 TYR   0.001   0.001   TYR K  10 
 PHE   0.006   0.001   PHE D  19 
 HIS   0.005   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 2970)
  covalent geometry    : angle       0.42867 ( 3970)
  hydrogen bonds       : bond        0.31639 (   16)
  hydrogen bonds       : angle      10.37197 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.6486 (mmp-170)
REVERT: A   27 ASN cc_start: 0.8497 (m-40) cc_final: 0.8265 (m110)
REVERT: B    3 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7504 (tp30)
REVERT: B    5 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.6673 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7636 (mtp85)
REVERT: C    7 ASP cc_start: 0.8358 (m-30) cc_final: 0.8157 (m-30)
REVERT: D   11 GLU cc_start: 0.8388 (pt0) cc_final: 0.7995 (pt0)
REVERT: E    5 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.7960 (tpp80)
REVERT: F    5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8087 (tpp80)
REVERT: F   13 HIS cc_start: 0.7885 (m90) cc_final: 0.7630 (m-70)
REVERT: G    5 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.8235 (ttm-80)
REVERT: G   28 LYS cc_start: 0.8975 (tttt) cc_final: 0.8656 (tttm)
REVERT: I    8 SER cc_start: 0.8898 (m) cc_final: 0.8548 (m)
REVERT: I   11 GLU cc_start: 0.8275 (pt0) cc_final: 0.8009 (pt0)
REVERT: I   28 LYS cc_start: 0.9122 (tttt) cc_final: 0.8849 (tttm)
REVERT: J    5 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.5867 (ppt170)
REVERT: J   28 LYS cc_start: 0.9081 (tttt) cc_final: 0.8113 (tppt)
REVERT: K    5 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.6282 (pmt170)
REVERT: K   11 GLU cc_start: 0.8203 (pt0) cc_final: 0.7918 (pt0)
REVERT: K   28 LYS cc_start: 0.8996 (tttt) cc_final: 0.8220 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.9155
  time to fit residues: 119.1576
Evaluate side-chains
  108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  15 GLN
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.095659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.087971 restraints weight = 14525.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.49
r_work: 0.3502 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   2970  Z= 0.273
  Angle     :  0.568   3.809   3970  Z= 0.330
  Chirality :  0.051   0.152    400
  Planarity :  0.002   0.011    530
  Dihedral  :  6.548  20.891    390
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.55 %
    Favored  : 81.72 %
  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: -2.16 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A   5 
 TYR   0.013   0.001   TYR I  10 
 PHE   0.008   0.001   PHE C  19 
 HIS   0.004   0.001   HIS E  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 2970)
  covalent geometry    : angle       0.56771 ( 3970)
  hydrogen bonds       : bond        0.10108 (   16)
  hydrogen bonds       : angle       6.19054 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.6761 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9311 (tttt) cc_final: 0.9021 (tttp)
REVERT: B    5 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.7154 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.8063 (mtp85)
REVERT: D   11 GLU cc_start: 0.8292 (pt0) cc_final: 0.7985 (pt0)
REVERT: F    5 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8363 (tpp80)
REVERT: I    1 ASP cc_start: 0.7764 (p0) cc_final: 0.7472 (p0)
REVERT: I    8 SER cc_start: 0.8883 (m) cc_final: 0.8348 (m)
REVERT: I   11 GLU cc_start: 0.8476 (pt0) cc_final: 0.8108 (pt0)
REVERT: I   28 LYS cc_start: 0.9234 (tttt) cc_final: 0.8964 (tttp)
REVERT: J    5 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.6137 (ppt170)
REVERT: J   10 TYR cc_start: 0.8560 (t80) cc_final: 0.8330 (t80)
REVERT: J   11 GLU cc_start: 0.8278 (pt0) cc_final: 0.7820 (mm-30)
REVERT: J   28 LYS cc_start: 0.9230 (tttt) cc_final: 0.8382 (tppt)
REVERT: K    5 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.6572 (pmt170)
REVERT: K   28 LYS cc_start: 0.9157 (tttt) cc_final: 0.8388 (tppt)
  outliers start: 5
  outliers final: 1
  residues processed: 116
  average time/residue: 1.1238
  time to fit residues: 133.2258
Evaluate side-chains
  108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.094243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.086658 restraints weight = 14997.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.46
r_work: 0.3535 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2970  Z= 0.237
  Angle     :  0.501   3.498   3970  Z= 0.293
  Chirality :  0.050   0.139    400
  Planarity :  0.002   0.016    530
  Dihedral  :  6.287  20.312    390
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.00 %
    Favored  : 76.55 %
  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: -2.29 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   5 
 TYR   0.012   0.002   TYR G  10 
 PHE   0.005   0.001   PHE E  19 
 HIS   0.005   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 2970)
  covalent geometry    : angle       0.50097 ( 3970)
  hydrogen bonds       : bond        0.09854 (   16)
  hydrogen bonds       : angle       6.03925 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.6782 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9308 (tttt) cc_final: 0.9046 (tttp)
REVERT: B    5 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.7184 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.8056 (mtp85)
REVERT: E   28 LYS cc_start: 0.9115 (tttt) cc_final: 0.8767 (ttpt)
REVERT: I    1 ASP cc_start: 0.8006 (p0) cc_final: 0.7652 (p0)
REVERT: I    8 SER cc_start: 0.8875 (m) cc_final: 0.8147 (m)
REVERT: I   11 GLU cc_start: 0.8310 (pt0) cc_final: 0.7876 (pt0)
REVERT: I   28 LYS cc_start: 0.9281 (tttt) cc_final: 0.9001 (tttp)
REVERT: J    5 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.6241 (ppt170)
REVERT: J   10 TYR cc_start: 0.8602 (t80) cc_final: 0.8316 (t80)
REVERT: J   11 GLU cc_start: 0.8135 (pt0) cc_final: 0.7888 (mm-30)
REVERT: J   28 LYS cc_start: 0.9296 (tttt) cc_final: 0.8469 (tppt)
REVERT: K    5 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.6629 (pmt170)
REVERT: K   28 LYS cc_start: 0.9137 (tttt) cc_final: 0.8426 (tppt)
  outliers start: 10
  outliers final: 7
  residues processed: 112
  average time/residue: 0.9769
  time to fit residues: 111.9792
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
C  15 GLN
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.098144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.089794 restraints weight = 14409.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.44
r_work: 0.3532 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2970  Z= 0.209
  Angle     :  0.516   3.764   3970  Z= 0.300
  Chirality :  0.050   0.143    400
  Planarity :  0.002   0.021    530
  Dihedral  :  6.116  19.090    390
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.72 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I   5 
 TYR   0.012   0.002   TYR I  10 
 PHE   0.005   0.001   PHE C  19 
 HIS   0.005   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 2970)
  covalent geometry    : angle       0.51591 ( 3970)
  hydrogen bonds       : bond        0.08581 (   16)
  hydrogen bonds       : angle       5.94468 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.6714 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9268 (tttt) cc_final: 0.9013 (tttp)
REVERT: B    5 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.7154 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8118 (mtp85)
REVERT: E   28 LYS cc_start: 0.9091 (tttt) cc_final: 0.8707 (ttpt)
REVERT: F   11 GLU cc_start: 0.8323 (pt0) cc_final: 0.7889 (pt0)
REVERT: I    1 ASP cc_start: 0.8064 (p0) cc_final: 0.7692 (p0)
REVERT: I   28 LYS cc_start: 0.9272 (tttt) cc_final: 0.8986 (tttm)
REVERT: J    5 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.6225 (ppt170)
REVERT: J   28 LYS cc_start: 0.9291 (tttt) cc_final: 0.8410 (tppt)
REVERT: K    5 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.6593 (pmt170)
REVERT: K   28 LYS cc_start: 0.9118 (tttt) cc_final: 0.8380 (tppt)
  outliers start: 9
  outliers final: 11
  residues processed: 111
  average time/residue: 0.9756
  time to fit residues: 111.0720
Evaluate side-chains
  117 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.096366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.088280 restraints weight = 14893.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.52
r_work: 0.3558 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2970  Z= 0.151
  Angle     :  0.498   4.494   3970  Z= 0.287
  Chirality :  0.050   0.140    400
  Planarity :  0.002   0.015    530
  Dihedral  :  5.891  18.537    390
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.83 %
    Favored  : 72.41 %
  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: -2.35 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D   5 
 TYR   0.012   0.002   TYR G  10 
 PHE   0.004   0.001   PHE I   4 
 HIS   0.005   0.001   HIS I  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2970)
  covalent geometry    : angle       0.49845 ( 3970)
  hydrogen bonds       : bond        0.08092 (   16)
  hydrogen bonds       : angle       5.96831 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.6628 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9275 (tttt) cc_final: 0.9027 (tttp)
REVERT: B    5 ARG cc_start: 0.8417 (mtt-85) cc_final: 0.6859 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8082 (mtp85)
REVERT: E   28 LYS cc_start: 0.9101 (tttt) cc_final: 0.8755 (ttpt)
REVERT: F   11 GLU cc_start: 0.8162 (pt0) cc_final: 0.7785 (pt0)
REVERT: I    1 ASP cc_start: 0.8110 (p0) cc_final: 0.7788 (p0)
REVERT: I   28 LYS cc_start: 0.9247 (tttt) cc_final: 0.8960 (tttp)
REVERT: J    5 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.6176 (ppt170)
REVERT: J   28 LYS cc_start: 0.9303 (tttt) cc_final: 0.8404 (tppt)
REVERT: K    5 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.6616 (pmt170)
REVERT: K   28 LYS cc_start: 0.9134 (tttt) cc_final: 0.8383 (tppt)
  outliers start: 8
  outliers final: 7
  residues processed: 105
  average time/residue: 0.9571
  time to fit residues: 102.9747
Evaluate side-chains
  111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.094453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.086219 restraints weight = 15058.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.58
r_work: 0.3543 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   2970  Z= 0.225
  Angle     :  0.516   5.182   3970  Z= 0.300
  Chirality :  0.050   0.145    400
  Planarity :  0.002   0.014    530
  Dihedral  :  6.035  18.526    390
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 26.55 %
    Favored  : 70.34 %
  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: -2.55 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.011   0.001   TYR I  10 
 PHE   0.009   0.001   PHE I   4 
 HIS   0.005   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 2970)
  covalent geometry    : angle       0.51617 ( 3970)
  hydrogen bonds       : bond        0.08814 (   16)
  hydrogen bonds       : angle       6.06419 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.6762 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9273 (tttt) cc_final: 0.9019 (tttp)
REVERT: E   28 LYS cc_start: 0.9142 (tttt) cc_final: 0.8763 (ttpt)
REVERT: F   11 GLU cc_start: 0.8184 (pt0) cc_final: 0.7850 (pt0)
REVERT: G   23 ASP cc_start: 0.7918 (m-30) cc_final: 0.7389 (m-30)
REVERT: I    1 ASP cc_start: 0.8206 (p0) cc_final: 0.7886 (p0)
REVERT: I   28 LYS cc_start: 0.9272 (tttt) cc_final: 0.8981 (tttp)
REVERT: J    5 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.6193 (ppt170)
REVERT: J   28 LYS cc_start: 0.9272 (tttt) cc_final: 0.8343 (tppt)
REVERT: K    5 ARG cc_start: 0.8702 (mtt-85) cc_final: 0.6632 (pmt170)
REVERT: K   28 LYS cc_start: 0.9153 (tttt) cc_final: 0.8386 (tppt)
  outliers start: 9
  outliers final: 8
  residues processed: 107
  average time/residue: 0.9974
  time to fit residues: 109.5441
Evaluate side-chains
  114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 29 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.096281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.087979 restraints weight = 14999.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.61
r_work: 0.3560 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2970  Z= 0.192
  Angle     :  0.541   5.315   3970  Z= 0.309
  Chirality :  0.050   0.140    400
  Planarity :  0.002   0.018    530
  Dihedral  :  5.925  18.658    390
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 27.59 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F   5 
 TYR   0.012   0.002   TYR J  10 
 PHE   0.009   0.001   PHE I   4 
 HIS   0.004   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 2970)
  covalent geometry    : angle       0.54057 ( 3970)
  hydrogen bonds       : bond        0.08181 (   16)
  hydrogen bonds       : angle       6.03353 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.6838 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9271 (tttt) cc_final: 0.9020 (tttp)
REVERT: D    3 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: E    8 SER cc_start: 0.8923 (m) cc_final: 0.8275 (t)
REVERT: E   28 LYS cc_start: 0.9125 (tttt) cc_final: 0.8763 (ttpt)
REVERT: F   11 GLU cc_start: 0.8171 (pt0) cc_final: 0.7903 (pt0)
REVERT: G   23 ASP cc_start: 0.7906 (m-30) cc_final: 0.7411 (m-30)
REVERT: I    1 ASP cc_start: 0.8159 (p0) cc_final: 0.7842 (p0)
REVERT: I   28 LYS cc_start: 0.9283 (tttt) cc_final: 0.8997 (tttm)
REVERT: J    5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.6206 (ppt170)
REVERT: J   28 LYS cc_start: 0.9331 (tttt) cc_final: 0.8430 (tppt)
REVERT: K    5 ARG cc_start: 0.8654 (mtt-85) cc_final: 0.6621 (pmt170)
REVERT: K   28 LYS cc_start: 0.9146 (tttt) cc_final: 0.8378 (tppt)
  outliers start: 9
  outliers final: 8
  residues processed: 105
  average time/residue: 1.0702
  time to fit residues: 115.0348
Evaluate side-chains
  112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue    5 ARG
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 10 optimal weight:    0.3980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.096153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.087781 restraints weight = 14688.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.62
r_work: 0.3576 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   2970  Z= 0.212
  Angle     :  0.534   6.083   3970  Z= 0.308
  Chirality :  0.050   0.141    400
  Planarity :  0.002   0.013    530
  Dihedral  :  5.963  18.448    390
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 30.34 %
    Favored  : 67.24 %
  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: -2.63 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B   5 
 TYR   0.012   0.001   TYR I  10 
 PHE   0.012   0.001   PHE I   4 
 HIS   0.005   0.001   HIS I  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 2970)
  covalent geometry    : angle       0.53444 ( 3970)
  hydrogen bonds       : bond        0.08462 (   16)
  hydrogen bonds       : angle       6.12079 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.9298 (tttt) cc_final: 0.9056 (tttp)
REVERT: E   28 LYS cc_start: 0.9171 (tttt) cc_final: 0.8831 (ttpt)
REVERT: F   11 GLU cc_start: 0.8119 (pt0) cc_final: 0.7873 (pt0)
REVERT: G   23 ASP cc_start: 0.7864 (m-30) cc_final: 0.7369 (m-30)
REVERT: I    1 ASP cc_start: 0.8230 (p0) cc_final: 0.7881 (p0)
REVERT: I   28 LYS cc_start: 0.9301 (tttt) cc_final: 0.9022 (tttp)
REVERT: J    5 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.6240 (ppt170)
REVERT: J   28 LYS cc_start: 0.9346 (tttt) cc_final: 0.8477 (tppt)
REVERT: K    5 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.6670 (pmt170)
REVERT: K   28 LYS cc_start: 0.9150 (tttt) cc_final: 0.8430 (tppt)
  outliers start: 7
  outliers final: 7
  residues processed: 106
  average time/residue: 1.0606
  time to fit residues: 115.4990
Evaluate side-chains
  110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.094730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.086836 restraints weight = 15069.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.57
r_work: 0.3573 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   2970  Z= 0.263
  Angle     :  0.549   5.180   3970  Z= 0.320
  Chirality :  0.050   0.138    400
  Planarity :  0.002   0.016    530
  Dihedral  :  6.146  20.125    390
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 31.38 %
    Favored  : 66.21 %
  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 aren not related in a simple way.
  whole: -2.81 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.013   0.002   TYR J  10 
 PHE   0.011   0.001   PHE I   4 
 HIS   0.005   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 2970)
  covalent geometry    : angle       0.54904 ( 3970)
  hydrogen bonds       : bond        0.09111 (   16)
  hydrogen bonds       : angle       6.13133 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.9310 (tttt) cc_final: 0.9052 (tttp)
REVERT: F   11 GLU cc_start: 0.8247 (pt0) cc_final: 0.7901 (pt0)
REVERT: I    1 ASP cc_start: 0.8189 (p0) cc_final: 0.7782 (p0)
REVERT: I   28 LYS cc_start: 0.9259 (tttt) cc_final: 0.8963 (tttm)
REVERT: J    5 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.6184 (ppt170)
REVERT: J   28 LYS cc_start: 0.9304 (tttt) cc_final: 0.8384 (tppt)
REVERT: K    5 ARG cc_start: 0.8693 (mtt-85) cc_final: 0.6541 (pmt170)
REVERT: K   28 LYS cc_start: 0.9106 (tttt) cc_final: 0.8330 (tppt)
  outliers start: 7
  outliers final: 8
  residues processed: 108
  average time/residue: 1.0529
  time to fit residues: 116.6962
Evaluate side-chains
  114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.097780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.089481 restraints weight = 14873.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.63
r_work: 0.3574 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2970  Z= 0.187
  Angle     :  0.603   6.496   3970  Z= 0.341
  Chirality :  0.051   0.140    400
  Planarity :  0.002   0.016    530
  Dihedral  :  5.990  19.819    390
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 32.41 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J   5 
 TYR   0.011   0.001   TYR I  10 
 PHE   0.007   0.001   PHE I   4 
 HIS   0.005   0.001   HIS G  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 2970)
  covalent geometry    : angle       0.60300 ( 3970)
  hydrogen bonds       : bond        0.08530 (   16)
  hydrogen bonds       : angle       6.08167 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.9293 (tttt) cc_final: 0.9031 (tttp)
REVERT: B    5 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.6869 (mmp-170)
REVERT: E    8 SER cc_start: 0.8852 (m) cc_final: 0.8211 (t)
REVERT: E   28 LYS cc_start: 0.9111 (tttt) cc_final: 0.8720 (ttpt)
REVERT: F    4 PHE cc_start: 0.7953 (m-10) cc_final: 0.7630 (m-80)
REVERT: F   11 GLU cc_start: 0.8276 (pt0) cc_final: 0.8027 (pt0)
REVERT: I   28 LYS cc_start: 0.9216 (tttt) cc_final: 0.8916 (tttp)
REVERT: J    5 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.6189 (ppt170)
REVERT: J   28 LYS cc_start: 0.9269 (tttt) cc_final: 0.8330 (tppt)
REVERT: K    5 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.6557 (pmt170)
REVERT: K   28 LYS cc_start: 0.9090 (tttt) cc_final: 0.8286 (tppt)
  outliers start: 7
  outliers final: 7
  residues processed: 105
  average time/residue: 1.0603
  time to fit residues: 114.2161
Evaluate side-chains
  111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain J residue    1 ASP
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0970
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.096843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.088447 restraints weight = 14636.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.63
r_work: 0.3604 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2970  Z= 0.174
  Angle     :  0.567   6.132   3970  Z= 0.321
  Chirality :  0.050   0.134    400
  Planarity :  0.002   0.016    530
  Dihedral  :  5.831  20.225    390
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 32.07 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.012   0.002   TYR G  10 
 PHE   0.007   0.001   PHE I   4 
 HIS   0.005   0.001   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 2970)
  covalent geometry    : angle       0.56686 ( 3970)
  hydrogen bonds       : bond        0.08009 (   16)
  hydrogen bonds       : angle       6.09516 (   48)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3370.27 seconds
wall clock time: 57 minutes 41.94 seconds (3461.94 seconds total)