Starting phenix.real_space_refine
on Sat Aug 23 04:46:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxt_15016/08_2025/7zxt_15016.map"
  }
  resolution = 2.9
  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=   0.001
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      90      5.16       5
     C    6534      2.51       5
     N    1668      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  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: 9924
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1654
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.61, per 1000 atoms: 0.16
  Number of scatterers: 9924
  At special positions: 0
  Unit cell: (105.294, 101.37, 91.56, 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      90     16.00
     O    1632      8.00
     N    1668      7.00
     C    6534      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 381.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      72.4% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
    Processing helix  chain 'A' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 10
    Processing helix  chain 'C' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL C  27 " --> pdb=" O   VAL C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 10
    Processing helix  chain 'D' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL D  27 " --> pdb=" O   VAL D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 10
    Processing helix  chain 'E' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL E  27 " --> pdb=" O   VAL E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 10
    Processing helix  chain 'F' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL F  27 " --> pdb=" O   VAL F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    751 hydrogen bonds defined for protein.
    2235 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: 1.60

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3006
        1.35 -     1.47: 2751
        1.47 -     1.60: 4293
        1.60 -     1.72: 0
        1.72 -     1.84: 132
  Bond restraints: 10182
  Sorted by residual:
  bond pdb=" C   THR B  86 "
       pdb=" N   PRO B  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR E  86 "
       pdb=" N   PRO E  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR F  86 "
       pdb=" N   PRO F  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.62e+00
  bond pdb=" C   THR D  86 "
       pdb=" N   PRO D  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.47e+00
  bond pdb=" C   THR C  86 "
       pdb=" N   PRO C  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.42e+00
  ... (remaining 10177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 13433
        1.47 -     2.93: 331
        2.93 -     4.40: 54
        4.40 -     5.87: 30
        5.87 -     7.34: 12
  Bond angle restraints: 13860
  Sorted by residual:
  angle pdb=" N   ILE A  20 "
        pdb=" CA  ILE A  20 "
        pdb=" C   ILE A  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.02    4.10 8.40e-01 1.42e+00 2.38e+01
  angle pdb=" N   ILE D  20 "
        pdb=" CA  ILE D  20 "
        pdb=" C   ILE D  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE E  20 "
        pdb=" CA  ILE E  20 "
        pdb=" C   ILE E  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE C  20 "
        pdb=" CA  ILE C  20 "
        pdb=" C   ILE C  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  angle pdb=" N   ILE F  20 "
        pdb=" CA  ILE F  20 "
        pdb=" C   ILE F  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  ... (remaining 13855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 5409
       14.98 -    29.96: 440
       29.96 -    44.94: 127
       44.94 -    59.92: 12
       59.92 -    74.90: 6
  Dihedral angle restraints: 5994
    sinusoidal: 2340
      harmonic: 3654
  Sorted by residual:
  dihedral pdb=" CA  CYS E 179 "
           pdb=" C   CYS E 179 "
           pdb=" N   PHE E 180 "
           pdb=" CA  PHE E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS B 179 "
           pdb=" C   CYS B 179 "
           pdb=" N   PHE B 180 "
           pdb=" CA  PHE B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS F 179 "
           pdb=" C   CYS F 179 "
           pdb=" N   PHE F 180 "
           pdb=" CA  PHE F 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.81  -30.19     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 5991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1157
       0.041 -    0.081: 399
       0.081 -    0.122: 64
       0.122 -    0.162: 6
       0.162 -    0.203: 18
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  VAL F  13 "
            pdb=" CA  VAL F  13 "
            pdb=" CG1 VAL F  13 "
            pdb=" CG2 VAL F  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL D  13 "
            pdb=" CA  VAL D  13 "
            pdb=" CG1 VAL D  13 "
            pdb=" CG2 VAL D  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  VAL A  13 "
            pdb=" CA  VAL A  13 "
            pdb=" CG1 VAL A  13 "
            pdb=" CG2 VAL A  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 183 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.48e+00
        pdb=" N   PRO F 184 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO F 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 183 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 184 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 183 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO C 184 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 126
        2.70 -     3.25: 10088
        3.25 -     3.80: 16732
        3.80 -     4.35: 19610
        4.35 -     4.90: 33380
  Nonbonded interactions: 79936
  Sorted by model distance:
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   ILE C  71 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE D  71 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE B  71 "
            pdb=" OH  TYR B 157 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ILE F  71 "
            pdb=" OH  TYR F 157 "
     model   vdw
     2.148 3.040
  ... (remaining 79931 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             3.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.800
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.003   0.035  10200  Z= 0.148
  Angle     :  0.636   7.337  13896  Z= 0.367
  Chirality :  0.043   0.203   1644
  Planarity :  0.003   0.030   1662
  Dihedral  : 12.065  74.901   3564
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.47 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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:  3.83 (0.24), residues: 1212
  helix:  3.93 (0.15), residues: 876
  sheet:  1.68 (0.55), residues: 60
  loop : -2.43 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  32 
 TYR   0.007   0.001   TYR B 135 
 PHE   0.008   0.001   PHE E  51 
 TRP   0.013   0.002   TRP D  44 
 HIS   0.002   0.000   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10182)
  covalent geometry    : angle       0.62580 (13860)
  SS BOND              : bond        0.00711 (   18)
  SS BOND              : angle       2.33027 (   36)
  hydrogen bonds       : bond        0.07917 (  751)
  hydrogen bonds       : angle       3.36008 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.410 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.6671
  time to fit residues: 169.7194
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  99 GLN
D  97 HIS
E  99 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.095121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.066398 restraints weight = 19817.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.37
r_work: 0.2790 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10200  Z= 0.211
  Angle     :  0.638   8.967  13896  Z= 0.334
  Chirality :  0.043   0.166   1644
  Planarity :  0.004   0.033   1662
  Dihedral  :  4.465  31.181   1350
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  2.97 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.68 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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:  3.58 (0.23), residues: 1212
  helix:  3.82 (0.14), residues: 876
  sheet:  0.35 (0.56), residues: 72
  loop : -2.60 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  22 
 TYR   0.010   0.001   TYR B 151 
 PHE   0.012   0.002   PHE D 180 
 TRP   0.006   0.001   TRP C 132 
 HIS   0.010   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (10182)
  covalent geometry    : angle       0.62927 (13860)
  SS BOND              : bond        0.00976 (   18)
  SS BOND              : angle       2.20704 (   36)
  hydrogen bonds       : bond        0.04218 (  751)
  hydrogen bonds       : angle       3.13737 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.433 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.8161 (m-30) cc_final: 0.7913 (m-30)
REVERT: D  211 TYR cc_start: 0.8588 (t80) cc_final: 0.8385 (t80)
REVERT: E   66 ASP cc_start: 0.8165 (m-30) cc_final: 0.7918 (m-30)
  outliers start: 27
  outliers final: 13
  residues processed: 181
  average time/residue: 0.6835
  time to fit residues: 131.5953
Evaluate side-chains
  173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:   30.0000
   chunk 14 optimal weight:    0.2980
   chunk 80 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.096639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.067684 restraints weight = 19898.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.41
r_work: 0.2814 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10200  Z= 0.150
  Angle     :  0.577   8.024  13896  Z= 0.302
  Chirality :  0.040   0.156   1644
  Planarity :  0.003   0.027   1662
  Dihedral  :  4.223  29.380   1350
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  2.97 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.30 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.77 (0.24), residues: 1212
  helix:  3.93 (0.14), residues: 882
  sheet:  1.36 (0.51), residues: 60
  loop : -2.70 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  75 
 TYR   0.008   0.001   TYR B 151 
 PHE   0.010   0.002   PHE F  31 
 TRP   0.005   0.001   TRP C 132 
 HIS   0.011   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10182)
  covalent geometry    : angle       0.57036 (13860)
  SS BOND              : bond        0.00886 (   18)
  SS BOND              : angle       1.80945 (   36)
  hydrogen bonds       : bond        0.03627 (  751)
  hydrogen bonds       : angle       3.06698 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: A  219 ARG cc_start: 0.1732 (OUTLIER) cc_final: 0.0695 (ttt180)
REVERT: B   99 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7580 (tm130)
REVERT: B  219 ARG cc_start: 0.1531 (OUTLIER) cc_final: 0.0541 (ttt180)
REVERT: C   66 ASP cc_start: 0.8243 (m-30) cc_final: 0.8022 (m-30)
REVERT: C  219 ARG cc_start: 0.1788 (OUTLIER) cc_final: 0.0818 (ttt180)
REVERT: D   66 ASP cc_start: 0.8323 (m-30) cc_final: 0.8121 (m-30)
REVERT: D   99 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: D  219 ARG cc_start: 0.1779 (OUTLIER) cc_final: 0.0743 (ttt180)
REVERT: E   99 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7562 (tm130)
REVERT: E  219 ARG cc_start: 0.1625 (OUTLIER) cc_final: 0.0619 (ttt180)
REVERT: F   66 ASP cc_start: 0.8244 (m-30) cc_final: 0.8027 (m-30)
REVERT: F  219 ARG cc_start: 0.1815 (OUTLIER) cc_final: 0.0854 (ttt180)
  outliers start: 19
  outliers final: 4
  residues processed: 174
  average time/residue: 0.7031
  time to fit residues: 130.1108
Evaluate side-chains
  160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.094940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.065885 restraints weight = 20241.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.41
r_work: 0.2781 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10200  Z= 0.198
  Angle     :  0.601   8.945  13896  Z= 0.318
  Chirality :  0.042   0.156   1644
  Planarity :  0.003   0.020   1662
  Dihedral  :  4.392  29.057   1350
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.64 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.66 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.36 (0.23), residues: 1212
  helix:  3.65 (0.15), residues: 876
  sheet:  1.46 (0.51), residues: 60
  loop : -2.83 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  75 
 TYR   0.011   0.001   TYR D 151 
 PHE   0.009   0.002   PHE B  68 
 TRP   0.004   0.001   TRP C 132 
 HIS   0.003   0.001   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (10182)
  covalent geometry    : angle       0.59276 (13860)
  SS BOND              : bond        0.00941 (   18)
  SS BOND              : angle       2.02419 (   36)
  hydrogen bonds       : bond        0.04058 (  751)
  hydrogen bonds       : angle       3.15640 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   99 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7524 (tm130)
REVERT: A  219 ARG cc_start: 0.1986 (OUTLIER) cc_final: 0.0824 (ttt180)
REVERT: B   99 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7597 (tm130)
REVERT: B  219 ARG cc_start: 0.1878 (OUTLIER) cc_final: 0.0707 (ttt180)
REVERT: C   66 ASP cc_start: 0.8214 (m-30) cc_final: 0.8007 (m-30)
REVERT: C  153 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8622 (t80)
REVERT: C  219 ARG cc_start: 0.2009 (OUTLIER) cc_final: 0.0908 (ttt180)
REVERT: D   99 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7528 (tm130)
REVERT: D  219 ARG cc_start: 0.1974 (OUTLIER) cc_final: 0.0844 (ttt180)
REVERT: E   99 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7602 (tm130)
REVERT: E  219 ARG cc_start: 0.1873 (OUTLIER) cc_final: 0.0715 (ttt180)
REVERT: F   66 ASP cc_start: 0.8232 (m-30) cc_final: 0.8005 (m-30)
REVERT: F  153 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (t80)
REVERT: F  219 ARG cc_start: 0.2010 (OUTLIER) cc_final: 0.0898 (ttt180)
  outliers start: 32
  outliers final: 13
  residues processed: 182
  average time/residue: 0.6955
  time to fit residues: 134.7188
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  153 PHE
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0980
   chunk 24 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.098862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.069991 restraints weight = 20027.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.45
r_work: 0.2860 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10200  Z= 0.116
  Angle     :  0.549   6.712  13896  Z= 0.292
  Chirality :  0.039   0.148   1644
  Planarity :  0.002   0.015   1662
  Dihedral  :  4.010  26.715   1350
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.56 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.82 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.85 (0.24), residues: 1212
  helix:  4.01 (0.15), residues: 882
  sheet:  1.08 (0.51), residues: 60
  loop : -2.67 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  75 
 TYR   0.007   0.001   TYR E 211 
 PHE   0.009   0.001   PHE C  31 
 TRP   0.005   0.001   TRP C 132 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10182)
  covalent geometry    : angle       0.54464 (13860)
  SS BOND              : bond        0.00765 (   18)
  SS BOND              : angle       1.52424 (   36)
  hydrogen bonds       : bond        0.03151 (  751)
  hydrogen bonds       : angle       2.99647 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8147 (m-30) cc_final: 0.7932 (m-30)
REVERT: A   99 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7537 (tm130)
REVERT: A  219 ARG cc_start: 0.1865 (OUTLIER) cc_final: 0.0879 (ttt180)
REVERT: B   22 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7712 (ptp90)
REVERT: B   66 ASP cc_start: 0.8219 (m-30) cc_final: 0.8003 (m-30)
REVERT: B   99 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7550 (tm130)
REVERT: B  219 ARG cc_start: 0.1712 (OUTLIER) cc_final: 0.0703 (ttt180)
REVERT: C   66 ASP cc_start: 0.8257 (m-30) cc_final: 0.7994 (m-30)
REVERT: C  219 ARG cc_start: 0.1878 (OUTLIER) cc_final: 0.0893 (ttt180)
REVERT: D   66 ASP cc_start: 0.8218 (m-30) cc_final: 0.7998 (m-30)
REVERT: D   99 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7539 (tm130)
REVERT: D  219 ARG cc_start: 0.1835 (OUTLIER) cc_final: 0.0861 (ttt180)
REVERT: E   66 ASP cc_start: 0.8237 (m-30) cc_final: 0.8017 (m-30)
REVERT: E   99 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7536 (tm130)
REVERT: E  219 ARG cc_start: 0.1744 (OUTLIER) cc_final: 0.0731 (ttt180)
REVERT: F   66 ASP cc_start: 0.8255 (m-30) cc_final: 0.7990 (m-30)
REVERT: F  219 ARG cc_start: 0.1865 (OUTLIER) cc_final: 0.0877 (ttt180)
  outliers start: 24
  outliers final: 16
  residues processed: 177
  average time/residue: 0.7220
  time to fit residues: 135.6690
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  126 HIS
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  126 HIS
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 89 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.097689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.068717 restraints weight = 20241.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.46
r_work: 0.2845 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10200  Z= 0.135
  Angle     :  0.565   7.031  13896  Z= 0.299
  Chirality :  0.040   0.150   1644
  Planarity :  0.003   0.015   1662
  Dihedral  :  4.016  25.838   1350
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.56 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.08 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.68 (0.24), residues: 1212
  helix:  3.90 (0.15), residues: 882
  sheet:  1.01 (0.52), residues: 60
  loop : -2.77 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  75 
 TYR   0.010   0.001   TYR D 171 
 PHE   0.008   0.001   PHE C  31 
 TRP   0.004   0.001   TRP C 132 
 HIS   0.002   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10182)
  covalent geometry    : angle       0.56024 (13860)
  SS BOND              : bond        0.00723 (   18)
  SS BOND              : angle       1.58994 (   36)
  hydrogen bonds       : bond        0.03343 (  751)
  hydrogen bonds       : angle       2.98549 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8174 (m-30) cc_final: 0.7956 (m-30)
REVERT: A   99 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7575 (tm130)
REVERT: A  219 ARG cc_start: 0.1998 (OUTLIER) cc_final: 0.0931 (ttt180)
REVERT: B   66 ASP cc_start: 0.8192 (m-30) cc_final: 0.7977 (m-30)
REVERT: B   99 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7610 (tm130)
REVERT: B  219 ARG cc_start: 0.1889 (OUTLIER) cc_final: 0.0807 (ttt180)
REVERT: C   66 ASP cc_start: 0.8224 (m-30) cc_final: 0.7989 (m-30)
REVERT: C  219 ARG cc_start: 0.2075 (OUTLIER) cc_final: 0.0991 (ttt180)
REVERT: D   99 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7581 (tm130)
REVERT: D  219 ARG cc_start: 0.1983 (OUTLIER) cc_final: 0.0926 (ttt180)
REVERT: E   66 ASP cc_start: 0.8202 (m-30) cc_final: 0.7984 (m-30)
REVERT: E   99 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7597 (tm130)
REVERT: E  219 ARG cc_start: 0.1910 (OUTLIER) cc_final: 0.0834 (ttt180)
REVERT: F   66 ASP cc_start: 0.8231 (m-30) cc_final: 0.7993 (m-30)
REVERT: F  219 ARG cc_start: 0.2054 (OUTLIER) cc_final: 0.0990 (ttt180)
  outliers start: 24
  outliers final: 16
  residues processed: 174
  average time/residue: 0.7185
  time to fit residues: 132.8568
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.096079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.067031 restraints weight = 20093.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.44
r_work: 0.2812 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10200  Z= 0.156
  Angle     :  0.590   7.616  13896  Z= 0.312
  Chirality :  0.040   0.148   1644
  Planarity :  0.003   0.016   1662
  Dihedral  :  4.111  25.862   1350
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  2.89 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.81 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.55 (0.24), residues: 1212
  helix:  3.77 (0.15), residues: 882
  sheet:  1.23 (0.54), residues: 60
  loop : -2.80 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  75 
 TYR   0.009   0.001   TYR B 151 
 PHE   0.008   0.001   PHE C  68 
 TRP   0.004   0.001   TRP C 132 
 HIS   0.002   0.001   HIS B 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10182)
  covalent geometry    : angle       0.58398 (13860)
  SS BOND              : bond        0.00765 (   18)
  SS BOND              : angle       1.74504 (   36)
  hydrogen bonds       : bond        0.03600 (  751)
  hydrogen bonds       : angle       3.06757 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8111 (m-30) cc_final: 0.7908 (m-30)
REVERT: A   99 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7267 (tm130)
REVERT: A  219 ARG cc_start: 0.1957 (OUTLIER) cc_final: 0.0915 (ttt180)
REVERT: B   66 ASP cc_start: 0.8166 (m-30) cc_final: 0.7938 (m-30)
REVERT: B   99 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7501 (tm130)
REVERT: B  219 ARG cc_start: 0.1889 (OUTLIER) cc_final: 0.0835 (ttt180)
REVERT: C   66 ASP cc_start: 0.8179 (m-30) cc_final: 0.7940 (m-30)
REVERT: C  219 ARG cc_start: 0.2014 (OUTLIER) cc_final: 0.0961 (ttt180)
REVERT: D   66 ASP cc_start: 0.8014 (m-30) cc_final: 0.7807 (m-30)
REVERT: D   99 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7283 (tm130)
REVERT: D  219 ARG cc_start: 0.1945 (OUTLIER) cc_final: 0.0916 (ttt180)
REVERT: E   66 ASP cc_start: 0.8174 (m-30) cc_final: 0.7944 (m-30)
REVERT: E   99 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7559 (tm130)
REVERT: E  219 ARG cc_start: 0.1900 (OUTLIER) cc_final: 0.0850 (ttt180)
REVERT: F   66 ASP cc_start: 0.8180 (m-30) cc_final: 0.7927 (m-30)
REVERT: F  219 ARG cc_start: 0.1994 (OUTLIER) cc_final: 0.0943 (ttt180)
  outliers start: 27
  outliers final: 16
  residues processed: 171
  average time/residue: 0.7163
  time to fit residues: 130.1563
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  146 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 75 optimal weight:    0.0980
   chunk 118 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 108 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
B  61 ASN
C  61 ASN
D  61 ASN
E  61 ASN
F  61 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.099593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.070606 restraints weight = 19962.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.48
r_work: 0.2898 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10200  Z= 0.116
  Angle     :  0.575   6.994  13896  Z= 0.302
  Chirality :  0.039   0.148   1644
  Planarity :  0.003   0.016   1662
  Dihedral  :  3.838  24.535   1350
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  2.81 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.80 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.82 (0.24), residues: 1212
  helix:  3.99 (0.15), residues: 882
  sheet:  1.28 (0.60), residues: 60
  loop : -2.76 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  75 
 TYR   0.009   0.001   TYR E 211 
 PHE   0.008   0.001   PHE F  31 
 TRP   0.005   0.001   TRP C 132 
 HIS   0.001   0.000   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10182)
  covalent geometry    : angle       0.57213 (13860)
  SS BOND              : bond        0.00618 (   18)
  SS BOND              : angle       1.33850 (   36)
  hydrogen bonds       : bond        0.02986 (  751)
  hydrogen bonds       : angle       2.96115 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8131 (m-30) cc_final: 0.7889 (m-30)
REVERT: A  219 ARG cc_start: 0.2083 (OUTLIER) cc_final: 0.1053 (ttt180)
REVERT: B   66 ASP cc_start: 0.8245 (m-30) cc_final: 0.7993 (m-30)
REVERT: B   99 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: B  219 ARG cc_start: 0.2029 (OUTLIER) cc_final: 0.1022 (ttt180)
REVERT: C   66 ASP cc_start: 0.8215 (m-30) cc_final: 0.7950 (m-30)
REVERT: C  219 ARG cc_start: 0.2157 (OUTLIER) cc_final: 0.1150 (ttt180)
REVERT: D   66 ASP cc_start: 0.8076 (m-30) cc_final: 0.7842 (m-30)
REVERT: D  219 ARG cc_start: 0.2053 (OUTLIER) cc_final: 0.1023 (ttt180)
REVERT: E   66 ASP cc_start: 0.8228 (m-30) cc_final: 0.7984 (m-30)
REVERT: E   99 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: E  219 ARG cc_start: 0.2050 (OUTLIER) cc_final: 0.1017 (ttt180)
REVERT: F   66 ASP cc_start: 0.8235 (m-30) cc_final: 0.7964 (m-30)
REVERT: F  219 ARG cc_start: 0.2125 (OUTLIER) cc_final: 0.1121 (ttt180)
  outliers start: 25
  outliers final: 9
  residues processed: 179
  average time/residue: 0.7118
  time to fit residues: 135.3808
Evaluate side-chains
  156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.098023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.068768 restraints weight = 19950.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.50
r_work: 0.2864 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10200  Z= 0.137
  Angle     :  0.626   7.671  13896  Z= 0.331
  Chirality :  0.040   0.153   1644
  Planarity :  0.003   0.017   1662
  Dihedral  :  3.899  23.944   1350
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.05 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 23.06 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.76 (0.24), residues: 1212
  helix:  3.92 (0.15), residues: 882
  sheet:  1.42 (0.63), residues: 60
  loop : -2.70 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  75 
 TYR   0.012   0.001   TYR E 211 
 PHE   0.009   0.001   PHE E  31 
 TRP   0.004   0.001   TRP A  44 
 HIS   0.001   0.000   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10182)
  covalent geometry    : angle       0.62258 (13860)
  SS BOND              : bond        0.00657 (   18)
  SS BOND              : angle       1.48419 (   36)
  hydrogen bonds       : bond        0.03202 (  751)
  hydrogen bonds       : angle       3.02673 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8164 (m-30) cc_final: 0.7956 (m-30)
REVERT: B   66 ASP cc_start: 0.8231 (m-30) cc_final: 0.8009 (m-30)
REVERT: B   99 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7558 (tm-30)
REVERT: C   66 ASP cc_start: 0.8218 (m-30) cc_final: 0.7968 (m-30)
REVERT: E   66 ASP cc_start: 0.8223 (m-30) cc_final: 0.7995 (m-30)
REVERT: E   99 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: F   66 ASP cc_start: 0.8198 (m-30) cc_final: 0.7937 (m-30)
  outliers start: 18
  outliers final: 10
  residues processed: 160
  average time/residue: 0.6790
  time to fit residues: 115.4980
Evaluate side-chains
  144 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain F residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 101 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
D  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.099350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.070073 restraints weight = 19775.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.52
r_work: 0.2889 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10200  Z= 0.132
  Angle     :  0.641   8.052  13896  Z= 0.337
  Chirality :  0.040   0.153   1644
  Planarity :  0.003   0.020   1662
  Dihedral  :  3.918  23.503   1350
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.55 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 23.78 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.88 (0.24), residues: 1212
  helix:  3.97 (0.15), residues: 882
  sheet:  1.43 (0.65), residues: 60
  loop : -2.53 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.013   0.001   TYR E 211 
 PHE   0.008   0.001   PHE E  31 
 TRP   0.005   0.001   TRP F 132 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10182)
  covalent geometry    : angle       0.63761 (13860)
  SS BOND              : bond        0.00624 (   18)
  SS BOND              : angle       1.38277 (   36)
  hydrogen bonds       : bond        0.03071 (  751)
  hydrogen bonds       : angle       3.07479 ( 2235)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8174 (m-30) cc_final: 0.7953 (m-30)
REVERT: B   66 ASP cc_start: 0.8246 (m-30) cc_final: 0.8005 (m-30)
REVERT: C   66 ASP cc_start: 0.8218 (m-30) cc_final: 0.7953 (m-30)
REVERT: E   66 ASP cc_start: 0.8251 (m-30) cc_final: 0.8013 (m-30)
REVERT: F   66 ASP cc_start: 0.8213 (m-30) cc_final: 0.7961 (m-30)
  outliers start: 9
  outliers final: 10
  residues processed: 147
  average time/residue: 0.5919
  time to fit residues: 92.9649
Evaluate side-chains
  138 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain F residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.065715 restraints weight = 20083.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.44
r_work: 0.2780 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10200  Z= 0.220
  Angle     :  0.703   8.493  13896  Z= 0.370
  Chirality :  0.043   0.159   1644
  Planarity :  0.003   0.026   1662
  Dihedral  :  4.280  25.244   1350
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.88 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.60 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.53 (0.24), residues: 1212
  helix:  3.68 (0.15), residues: 876
  sheet:  1.75 (0.62), residues: 60
  loop : -2.47 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  75 
 TYR   0.017   0.002   TYR E 211 
 PHE   0.011   0.002   PHE A 190 
 TRP   0.004   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (10182)
  covalent geometry    : angle       0.69640 (13860)
  SS BOND              : bond        0.00845 (   18)
  SS BOND              : angle       2.04305 (   36)
  hydrogen bonds       : bond        0.04018 (  751)
  hydrogen bonds       : angle       3.35975 ( 2235)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3376.05 seconds
wall clock time: 58 minutes 29.13 seconds (3509.13 seconds total)