Starting phenix.real_space_refine
on Fri Aug 22 14:00:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b34_44125/08_2025/9b34_44125.cif"
  }
  resolution = 3.58
  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=   0.002 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      2      6.06       5
     S       4      5.16       5
     C    2281      2.51       5
     N     604      2.21       5
     O     726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3619
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1806
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "F"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1809
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 225}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.19, per 1000 atoms: 0.33
  Number of scatterers: 3619
  At special positions: 0
  Unit cell: (63.3889, 57.9941, 93.0603, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     Ca      2     19.99
     S       4     16.00
     O     726      8.00
     N     604      7.00
     C    2281      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 150.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN E1001 "
        pdb="ZN    ZN E1001 " - pdb=" NE2 HIS E  24 "
      pdb="  ZN F1001 "
        pdb="ZN    ZN F1001 " - pdb=" NE2 HIS F  24 "


  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  884

  Finding SS restraints...
    Secondary structure from input PDB file:
      1 helices and 10 sheets defined
      1.1% alpha, 36.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'E' and resid 14 through 18
      removed outlier: 3.809A  pdb=" N   GLY E  18 " --> pdb=" O   THR E  15 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 5 through 6
      removed outlier: 3.601A  pdb=" N   SER E  94 " --> pdb=" O   ALA E 211 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY E  92 " --> pdb=" O   PHE E 213 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER E 215 " --> pdb=" O   ARG E  90 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG E  90 " --> pdb=" O   SER E 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 6
      removed outlier: 3.601A  pdb=" N   SER E  94 " --> pdb=" O   ALA E 211 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY E  92 " --> pdb=" O   PHE E 213 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER E 215 " --> pdb=" O   ARG E  90 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG E  90 " --> pdb=" O   SER E 215 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL E 179 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 10
    Processing sheet with id=AA4, first strand: chain 'E' and resid 49 through 54
    Processing sheet with id=AA5, first strand: chain 'E' and resid 154 through 155
    Processing sheet with id=AA6, first strand: chain 'E' and resid 128 through 130
      removed outlier: 3.844A  pdb=" N   THR E 194 " --> pdb=" O   SER E 110 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 39
      removed outlier: 4.256A  pdb=" N   LYS F  36 " --> pdb=" O   ILE F  27 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE F 212 " --> pdb=" O   VAL F   7 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY F  92 " --> pdb=" O   PHE F 213 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   VAL F  91 " --> pdb=" O   PHE F 175 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LEU F 174 " --> pdb=" O   ILE F 141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 39
      removed outlier: 4.256A  pdb=" N   LYS F  36 " --> pdb=" O   ILE F  27 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE F 212 " --> pdb=" O   VAL F   7 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY F  92 " --> pdb=" O   PHE F 213 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL F 179 " --> pdb=" O   VAL F  89 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78
      removed outlier: 3.511A  pdb=" N   TYR F  77 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA F  50 " --> pdb=" O   PHE F 195 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE F  52 " --> pdb=" O   ALA F 193 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR F 194 " --> pdb=" O   SER F 110 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER F 108 " --> pdb=" O   THR F 196 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU F 198 " --> pdb=" O   ILE F 106 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ILE F 106 " --> pdb=" O   LEU F 198 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 77 through 78
      removed outlier: 3.511A  pdb=" N   TYR F  77 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA F  50 " --> pdb=" O   PHE F 195 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE F  52 " --> pdb=" O   ALA F 193 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR F 194 " --> pdb=" O   SER F 110 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER F 108 " --> pdb=" O   THR F 196 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU F 198 " --> pdb=" O   ILE F 106 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ILE F 106 " --> pdb=" O   LEU F 198 " (cutoff:3.500A)

    110 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1103
        1.34 -     1.45: 640
        1.45 -     1.57: 1948
        1.57 -     1.69: 0
        1.69 -     1.81: 8
  Bond restraints: 3699
  Sorted by residual:
  bond pdb=" CA  ASP F 208 "
       pdb=" C   ASP F 208 "
    ideal  model  delta    sigma   weight residual
    1.521  1.559 -0.037 1.14e-02 7.69e+03 1.08e+01
  bond pdb=" C   SER F  21 "
       pdb=" N   TYR F  22 "
    ideal  model  delta    sigma   weight residual
    1.327  1.296  0.031 1.39e-02 5.18e+03 4.88e+00
  bond pdb=" N   SER E 119 "
       pdb=" CA  SER E 119 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.026 1.29e-02 6.01e+03 4.19e+00
  bond pdb=" CB  ASN E  69 "
       pdb=" CG  ASN E  69 "
    ideal  model  delta    sigma   weight residual
    1.516  1.565 -0.049 2.50e-02 1.60e+03 3.85e+00
  bond pdb=" CA  ALA F 186 "
       pdb=" C   ALA F 186 "
    ideal  model  delta    sigma   weight residual
    1.523  1.549 -0.025 1.34e-02 5.57e+03 3.60e+00
  ... (remaining 3694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.63: 4961
        4.63 -     9.27: 74
        9.27 -    13.90: 7
       13.90 -    18.54: 0
       18.54 -    23.17: 2
  Bond angle restraints: 5044
  Sorted by residual:
  angle pdb=" N   GLY F  48 "
        pdb=" CA  GLY F  48 "
        pdb=" C   GLY F  48 "
      ideal   model   delta    sigma   weight residual
     113.18  133.23  -20.05 2.37e+00 1.78e-01 7.16e+01
  angle pdb=" N   GLY E  48 "
        pdb=" CA  GLY E  48 "
        pdb=" C   GLY E  48 "
      ideal   model   delta    sigma   weight residual
     115.33  138.50  -23.17 2.74e+00 1.33e-01 7.15e+01
  angle pdb=" N   ALA E 207 "
        pdb=" CA  ALA E 207 "
        pdb=" C   ALA E 207 "
      ideal   model   delta    sigma   weight residual
     107.20  118.76  -11.56 1.70e+00 3.46e-01 4.62e+01
  angle pdb=" N   ALA E 186 "
        pdb=" CA  ALA E 186 "
        pdb=" C   ALA E 186 "
      ideal   model   delta    sigma   weight residual
     110.80  122.94  -12.14 2.13e+00 2.20e-01 3.25e+01
  angle pdb=" N   ALA F 186 "
        pdb=" CA  ALA F 186 "
        pdb=" C   ALA F 186 "
      ideal   model   delta    sigma   weight residual
     110.80  122.84  -12.04 2.13e+00 2.20e-01 3.20e+01
  ... (remaining 5039 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.84: 1978
       14.84 -    29.69: 146
       29.69 -    44.53: 44
       44.53 -    59.38: 10
       59.38 -    74.22: 4
  Dihedral angle restraints: 2182
    sinusoidal: 812
      harmonic: 1370
  Sorted by residual:
  dihedral pdb=" CA  ALA E 207 "
           pdb=" C   ALA E 207 "
           pdb=" N   ASP E 208 "
           pdb=" CA  ASP E 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.71   70.29     0      5.00e+00 4.00e-02 1.98e+02
  dihedral pdb=" CA  VAL F  47 "
           pdb=" C   VAL F  47 "
           pdb=" N   GLY F  48 "
           pdb=" CA  GLY F  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  117.97   62.03     0      5.00e+00 4.00e-02 1.54e+02
  dihedral pdb=" CA  VAL E  47 "
           pdb=" C   VAL E  47 "
           pdb=" N   GLY E  48 "
           pdb=" CA  GLY E  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  121.49   58.51     0      5.00e+00 4.00e-02 1.37e+02
  ... (remaining 2179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 420
       0.067 -    0.133: 109
       0.133 -    0.200: 34
       0.200 -    0.266: 11
       0.266 -    0.333: 6
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CB  VAL F 187 "
            pdb=" CA  VAL F 187 "
            pdb=" CG1 VAL F 187 "
            pdb=" CG2 VAL F 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CB  VAL E 187 "
            pdb=" CA  VAL E 187 "
            pdb=" CG1 VAL E 187 "
            pdb=" CG2 VAL E 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CB  VAL F  75 "
            pdb=" CA  VAL F  75 "
            pdb=" CG1 VAL F  75 "
            pdb=" CG2 VAL F  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 577 not shown)

  Planarity restraints: 651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 141 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.35e+00
        pdb=" C   ILE F 141 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ILE F 141 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU F 142 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP E 208 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.98e+00
        pdb=" CG  ASP E 208 "   -0.049 2.00e-02 2.50e+03
        pdb=" OD1 ASP E 208 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP E 208 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 118 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.96e+00
        pdb=" C   ASN F 118 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ASN F 118 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER F 119 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 648 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 139
        2.68 -     3.23: 3433
        3.23 -     3.79: 5728
        3.79 -     4.34: 7350
        4.34 -     4.90: 12555
  Nonbonded interactions: 29205
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E  10 "
            pdb="ZN    ZN E1001 "
     model   vdw
     2.121 2.230
  nonbonded pdb=" OD1 ASP E  19 "
            pdb="ZN    ZN E1001 "
     model   vdw
     2.133 2.230
  nonbonded pdb=" OD2 ASP F  10 "
            pdb="ZN    ZN F1001 "
     model   vdw
     2.151 2.230
  nonbonded pdb=" OD1 ASP F  19 "
            pdb="ZN    ZN F1001 "
     model   vdw
     2.181 2.230
  nonbonded pdb=" OG  SER E 108 "
            pdb=" OG1 THR E 196 "
     model   vdw
     2.261 3.040
  ... (remaining 29200 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 147 through 1002))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.240
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
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      :  0.007   0.093   3701  Z= 0.338
  Angle     :  1.466  23.170   5044  Z= 0.788
  Chirality :  0.077   0.333    580
  Planarity :  0.009   0.060    651
  Dihedral  : 12.857  74.220   1298
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  1.91 %
    Allowed  : 23.62 %
    Favored  : 74.47 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.68 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.56 %

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: -5.95 (0.31), residues: 470
  helix:  None (None), residues: 0
  sheet: -4.50 (0.34), residues: 126
  loop : -4.04 (0.27), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG F 228 
 TYR   0.016   0.003   TYR E 176 
 PHE   0.036   0.005   PHE E 130 
 TRP   0.035   0.005   TRP E 182 
 HIS   0.004   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 3699)
  covalent geometry    : angle       1.46591 ( 5044)
  hydrogen bonds       : bond        0.32816 (   78)
  hydrogen bonds       : angle      13.93349 (  264)
  metal coordination   : bond        0.02763 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 ILE cc_start: 0.9158 (tt) cc_final: 0.8886 (mt)
REVERT: E   39 LYS cc_start: 0.8538 (tttt) cc_final: 0.8171 (tppp)
REVERT: E   53 ILE cc_start: 0.7856 (pp) cc_final: 0.7608 (mt)
REVERT: E   55 ASN cc_start: 0.8361 (p0) cc_final: 0.8143 (p0)
REVERT: E  126 LEU cc_start: 0.9085 (tp) cc_final: 0.8771 (tp)
REVERT: E  158 ARG cc_start: 0.6605 (mtp-110) cc_final: 0.5844 (ptm160)
REVERT: E  195 PHE cc_start: 0.7046 (t80) cc_final: 0.6783 (t80)
REVERT: E  228 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.5364 (mmt180)
REVERT: E  229 LEU cc_start: 0.8479 (mt) cc_final: 0.8220 (mt)
REVERT: F  126 LEU cc_start: 0.8408 (tp) cc_final: 0.8126 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0825
  time to fit residues: 13.9283
Evaluate side-chains
  79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0000
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
E  83 ASN
E 162 ASN
** F  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 131 ASN
F 162 ASN
F 180 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.162754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.145439 restraints weight = 6207.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.149912 restraints weight = 3422.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.152805 restraints weight = 2219.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.154706 restraints weight = 1578.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.156150 restraints weight = 1210.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3701  Z= 0.180
  Angle     :  1.028  18.864   5044  Z= 0.522
  Chirality :  0.054   0.190    580
  Planarity :  0.007   0.052    651
  Dihedral  : 10.832  52.473    500
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.55 %
    Favored  : 76.17 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.56 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.56 %

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: -5.50 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -4.09 (0.35), residues: 156
  loop : -3.60 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  90 
 TYR   0.017   0.002   TYR E  12 
 PHE   0.018   0.002   PHE F 128 
 TRP   0.035   0.002   TRP E 182 
 HIS   0.005   0.002   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3699)
  covalent geometry    : angle       1.02809 ( 5044)
  hydrogen bonds       : bond        0.04572 (   78)
  hydrogen bonds       : angle       7.61579 (  264)
  metal coordination   : bond        0.00543 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 ILE cc_start: 0.8850 (tt) cc_final: 0.8638 (mt)
REVERT: E  129 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6818 (ttp)
REVERT: E  139 ASP cc_start: 0.8527 (p0) cc_final: 0.8313 (p0)
REVERT: E  158 ARG cc_start: 0.6133 (mtp-110) cc_final: 0.5748 (mmm-85)
REVERT: E  228 ARG cc_start: 0.7184 (ptp-110) cc_final: 0.5263 (mpt180)
REVERT: E  229 LEU cc_start: 0.8301 (mt) cc_final: 0.8070 (mt)
REVERT: F   54 TYR cc_start: 0.7303 (t80) cc_final: 0.6820 (t80)
REVERT: F  126 LEU cc_start: 0.8594 (tp) cc_final: 0.8289 (tp)
REVERT: F  208 ASP cc_start: 0.3908 (t0) cc_final: 0.3547 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0665
  time to fit residues: 8.1985
Evaluate side-chains
  78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  129 MET
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue  180 HIS
Chi-restraints excluded: chain F residue  205 HIS
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0670
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
E  51 HIS
E 162 ASN
F  14 ASN
** F  24 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 = 0.4046 r_free = 0.4046 target = 0.150412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.132239 restraints weight = 6205.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136228 restraints weight = 3731.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.138976 restraints weight = 2545.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.140773 restraints weight = 1880.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.142212 restraints weight = 1482.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3701  Z= 0.154
  Angle     :  0.937  17.767   5044  Z= 0.477
  Chirality :  0.051   0.192    580
  Planarity :  0.006   0.043    651
  Dihedral  : 10.211  51.382    500
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 20.21 %
    Favored  : 78.51 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.80 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

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: -5.03 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.29 (0.42), residues: 136
  loop : -3.62 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F  90 
 TYR   0.008   0.001   TYR E  12 
 PHE   0.020   0.002   PHE E 191 
 TRP   0.026   0.002   TRP E 182 
 HIS   0.009   0.002   HIS F 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3699)
  covalent geometry    : angle       0.93745 ( 5044)
  hydrogen bonds       : bond        0.03918 (   78)
  hydrogen bonds       : angle       7.08910 (  264)
  metal coordination   : bond        0.00095 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: E   41 ASN cc_start: 0.8332 (t0) cc_final: 0.7981 (t0)
REVERT: E  162 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5804 (p0)
REVERT: E  228 ARG cc_start: 0.7095 (ptp-110) cc_final: 0.5370 (mpt180)
  outliers start: 16
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0615
  time to fit residues: 6.9772
Evaluate side-chains
  80 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  162 ASN
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0470
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.0082

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

Flipped N/Q/H residues before XYZ refinement:
E 153 ASN
E 180 HIS
** F  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.145475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.126117 restraints weight = 6360.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.130392 restraints weight = 3622.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133268 restraints weight = 2412.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.135267 restraints weight = 1763.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.136584 restraints weight = 1377.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3701  Z= 0.201
  Angle     :  0.951  16.776   5044  Z= 0.487
  Chirality :  0.053   0.187    580
  Planarity :  0.006   0.041    651
  Dihedral  : 10.203  52.798    500
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 19.92
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.77 %
    Favored  : 75.96 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.54 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.83 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.94 (0.43), residues: 138
  loop : -3.58 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 158 
 TYR   0.019   0.002   TYR F  12 
 PHE   0.015   0.002   PHE E 130 
 TRP   0.021   0.002   TRP E 182 
 HIS   0.006   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3699)
  covalent geometry    : angle       0.95117 ( 5044)
  hydrogen bonds       : bond        0.03743 (   78)
  hydrogen bonds       : angle       6.92204 (  264)
  metal coordination   : bond        0.00229 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6838 (mtt-85)
REVERT: E   41 ASN cc_start: 0.8554 (t0) cc_final: 0.8075 (t0)
REVERT: E  129 MET cc_start: 0.7219 (ttp) cc_final: 0.6739 (ttt)
REVERT: E  228 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.5374 (mpt180)
REVERT: F   94 SER cc_start: 0.8444 (t) cc_final: 0.7605 (p)
REVERT: F  145 ASP cc_start: 0.7190 (m-30) cc_final: 0.6807 (t0)
REVERT: F  208 ASP cc_start: 0.5270 (t0) cc_final: 0.4815 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0614
  time to fit residues: 6.6577
Evaluate side-chains
  91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   78 ASP
Chi-restraints excluded: chain F residue   81 LEU
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  205 HIS
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0322

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

Flipped N/Q/H residues before XYZ refinement:
** F  24 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.142481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.123973 restraints weight = 6229.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.127717 restraints weight = 3758.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.130320 restraints weight = 2585.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.132110 restraints weight = 1945.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.133576 restraints weight = 1555.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.6010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3701  Z= 0.192
  Angle     :  0.943  17.211   5044  Z= 0.479
  Chirality :  0.053   0.188    580
  Planarity :  0.006   0.041    651
  Dihedral  : 10.066  52.206    500
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 22.55 %
    Favored  : 76.38 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.52 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.69 (0.35), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.90 (0.43), residues: 140
  loop : -3.45 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  33 
 TYR   0.016   0.002   TYR F  12 
 PHE   0.018   0.002   PHE E 191 
 TRP   0.038   0.003   TRP E 182 
 HIS   0.007   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3699)
  covalent geometry    : angle       0.94338 ( 5044)
  hydrogen bonds       : bond        0.03558 (   78)
  hydrogen bonds       : angle       7.03446 (  264)
  metal coordination   : bond        0.00309 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: E   41 ASN cc_start: 0.8532 (t0) cc_final: 0.8171 (t0)
REVERT: E  129 MET cc_start: 0.7045 (ttp) cc_final: 0.6815 (ttt)
REVERT: E  232 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7522 (pp)
REVERT: F   94 SER cc_start: 0.8490 (t) cc_final: 0.7872 (p)
REVERT: F  145 ASP cc_start: 0.7024 (m-30) cc_final: 0.6683 (t0)
REVERT: F  208 ASP cc_start: 0.5351 (t0) cc_final: 0.4969 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0586
  time to fit residues: 7.2284
Evaluate side-chains
  85 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  205 HIS
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.144386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.126460 restraints weight = 6161.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.130084 restraints weight = 3738.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.132641 restraints weight = 2587.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.134486 restraints weight = 1943.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.135595 restraints weight = 1546.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.6446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3701  Z= 0.169
  Angle     :  0.920  15.892   5044  Z= 0.465
  Chirality :  0.051   0.176    580
  Planarity :  0.006   0.038    651
  Dihedral  :  9.751  46.520    500
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 23.62 %
    Favored  : 75.32 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 21.23 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.53 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.72 (0.44), residues: 140
  loop : -3.37 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  33 
 TYR   0.014   0.001   TYR F  12 
 PHE   0.023   0.002   PHE F 195 
 TRP   0.047   0.002   TRP E 182 
 HIS   0.007   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3699)
  covalent geometry    : angle       0.91960 ( 5044)
  hydrogen bonds       : bond        0.03473 (   78)
  hydrogen bonds       : angle       6.81236 (  264)
  metal coordination   : bond        0.00196 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   41 ASN cc_start: 0.8450 (t0) cc_final: 0.8022 (t0)
REVERT: E   51 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6056 (t70)
REVERT: E  232 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7626 (pp)
REVERT: F   94 SER cc_start: 0.8399 (t) cc_final: 0.7917 (p)
REVERT: F  145 ASP cc_start: 0.6891 (m-30) cc_final: 0.6640 (t0)
REVERT: F  208 ASP cc_start: 0.6063 (t0) cc_final: 0.5706 (m-30)
REVERT: F  223 SER cc_start: 0.6980 (OUTLIER) cc_final: 0.6712 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0577
  time to fit residues: 6.6657
Evaluate side-chains
  88 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  210 ILE
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** F  24 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.137618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.120388 restraints weight = 6312.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.123825 restraints weight = 3796.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.126206 restraints weight = 2626.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.127802 restraints weight = 1977.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.129207 restraints weight = 1585.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.6884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3701  Z= 0.261
  Angle     :  1.002  14.116   5044  Z= 0.513
  Chirality :  0.055   0.208    580
  Planarity :  0.006   0.050    651
  Dihedral  : 10.171  50.383    500
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 21.89
  Ramachandran Plot:
    Outliers :  1.49 %
    Allowed  : 23.40 %
    Favored  : 75.11 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 20.49 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.67 (0.35), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.80 (0.44), residues: 140
  loop : -3.48 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  33 
 TYR   0.021   0.002   TYR F  12 
 PHE   0.030   0.003   PHE F 195 
 TRP   0.052   0.003   TRP E 182 
 HIS   0.007   0.002   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 3699)
  covalent geometry    : angle       1.00168 ( 5044)
  hydrogen bonds       : bond        0.03665 (   78)
  hydrogen bonds       : angle       7.13789 (  264)
  metal coordination   : bond        0.00421 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6153 (t70)
REVERT: F   94 SER cc_start: 0.8342 (t) cc_final: 0.7630 (p)
REVERT: F  145 ASP cc_start: 0.6935 (m-30) cc_final: 0.6605 (t0)
REVERT: F  208 ASP cc_start: 0.6209 (t0) cc_final: 0.5728 (m-30)
REVERT: F  223 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7177 (t)
  outliers start: 26
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0620
  time to fit residues: 7.2984
Evaluate side-chains
  88 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   28 ASP
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   53 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   81 LEU
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  142 LEU
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  210 ILE
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.0050
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.142828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.125130 restraints weight = 6248.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.128868 restraints weight = 3688.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.131416 restraints weight = 2507.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.133118 restraints weight = 1864.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.134537 restraints weight = 1478.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.7111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3701  Z= 0.164
  Angle     :  0.946  14.713   5044  Z= 0.474
  Chirality :  0.052   0.227    580
  Planarity :  0.006   0.038    651
  Dihedral  :  9.655  46.257    500
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 18.80
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.34 %
    Favored  : 76.38 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 21.98 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.45 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.56 (0.47), residues: 140
  loop : -3.38 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  33 
 TYR   0.008   0.001   TYR F  12 
 PHE   0.031   0.002   PHE F 195 
 TRP   0.053   0.003   TRP E 182 
 HIS   0.006   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3699)
  covalent geometry    : angle       0.94558 ( 5044)
  hydrogen bonds       : bond        0.03280 (   78)
  hydrogen bonds       : angle       6.88714 (  264)
  metal coordination   : bond        0.00169 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6074 (t70)
REVERT: E  130 PHE cc_start: 0.7632 (m-80) cc_final: 0.7347 (m-80)
REVERT: E  208 ASP cc_start: 0.7083 (t0) cc_final: 0.6498 (t70)
REVERT: E  213 PHE cc_start: 0.8784 (p90) cc_final: 0.7810 (p90)
REVERT: F   64 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (m)
REVERT: F   94 SER cc_start: 0.8370 (t) cc_final: 0.7948 (p)
REVERT: F  223 SER cc_start: 0.7027 (OUTLIER) cc_final: 0.6662 (t)
  outliers start: 24
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0556
  time to fit residues: 6.3861
Evaluate side-chains
  83 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain F residue    5 VAL
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  142 LEU
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  210 ILE
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
F 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.141661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.123372 restraints weight = 6195.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.127050 restraints weight = 3698.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.129518 restraints weight = 2551.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.131423 restraints weight = 1936.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.132859 restraints weight = 1540.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.7358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3701  Z= 0.169
  Angle     :  0.942  14.248   5044  Z= 0.472
  Chirality :  0.052   0.220    580
  Planarity :  0.006   0.035    651
  Dihedral  :  9.433  46.249    500
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 23.19 %
    Favored  : 75.74 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 23.70 %
    Favored  : 71.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.48 (0.48), residues: 136
  loop : -3.35 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  33 
 TYR   0.010   0.001   TYR F  12 
 PHE   0.038   0.003   PHE F 195 
 TRP   0.052   0.003   TRP E 182 
 HIS   0.004   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3699)
  covalent geometry    : angle       0.94161 ( 5044)
  hydrogen bonds       : bond        0.03129 (   78)
  hydrogen bonds       : angle       6.77280 (  264)
  metal coordination   : bond        0.00168 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6007 (t70)
REVERT: E  130 PHE cc_start: 0.7576 (m-80) cc_final: 0.7323 (m-80)
REVERT: E  174 LEU cc_start: 0.8747 (mp) cc_final: 0.8352 (mt)
REVERT: E  208 ASP cc_start: 0.7078 (t0) cc_final: 0.6488 (t70)
REVERT: E  213 PHE cc_start: 0.8764 (p90) cc_final: 0.8033 (p90)
REVERT: F   25 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8433 (mm)
REVERT: F   94 SER cc_start: 0.8381 (t) cc_final: 0.7981 (p)
REVERT: F  208 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.5668 (m-30)
REVERT: F  223 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6699 (t)
  outliers start: 20
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0654
  time to fit residues: 7.4463
Evaluate side-chains
  89 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  208 ASP
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.142745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.123891 restraints weight = 6321.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127751 restraints weight = 3777.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.130437 restraints weight = 2595.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132238 restraints weight = 1950.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.133707 restraints weight = 1559.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.7638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3701  Z= 0.165
  Angle     :  0.947  14.028   5044  Z= 0.473
  Chirality :  0.052   0.218    580
  Planarity :  0.006   0.036    651
  Dihedral  :  9.314  46.197    500
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 24.47 %
    Favored  : 74.47 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.19 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.46 (0.49), residues: 136
  loop : -3.37 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  33 
 TYR   0.016   0.001   TYR F  12 
 PHE   0.024   0.002   PHE F 191 
 TRP   0.051   0.003   TRP E 182 
 HIS   0.005   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3699)
  covalent geometry    : angle       0.94719 ( 5044)
  hydrogen bonds       : bond        0.03149 (   78)
  hydrogen bonds       : angle       6.75771 (  264)
  metal coordination   : bond        0.00157 (    2)

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

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

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  940 Ramachandran restraints generated.
    470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.5977 (t70)
REVERT: E  130 PHE cc_start: 0.7581 (m-80) cc_final: 0.7305 (m-80)
REVERT: E  174 LEU cc_start: 0.8814 (mp) cc_final: 0.8480 (mt)
REVERT: E  208 ASP cc_start: 0.7092 (t0) cc_final: 0.6473 (t70)
REVERT: E  213 PHE cc_start: 0.8701 (p90) cc_final: 0.7965 (p90)
REVERT: F   64 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8133 (m)
REVERT: F   94 SER cc_start: 0.8563 (t) cc_final: 0.8054 (p)
REVERT: F  208 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.5743 (m-30)
REVERT: F  223 SER cc_start: 0.6968 (OUTLIER) cc_final: 0.6586 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0640
  time to fit residues: 7.3436
Evaluate side-chains
  89 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  210 ILE
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  208 ASP
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0070
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
F  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.144400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.126108 restraints weight = 6231.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.129899 restraints weight = 3722.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.132601 restraints weight = 2565.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.134396 restraints weight = 1917.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.135840 restraints weight = 1526.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.7750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3701  Z= 0.159
  Angle     :  0.941  14.143   5044  Z= 0.469
  Chirality :  0.051   0.218    580
  Planarity :  0.005   0.036    651
  Dihedral  :  9.146  45.351    500
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 23.62 %
    Favored  : 75.53 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.93 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.37 (0.50), residues: 130
  loop : -3.40 (0.29), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  33 
 TYR   0.017   0.001   TYR F  12 
 PHE   0.023   0.002   PHE F 191 
 TRP   0.048   0.003   TRP E 182 
 HIS   0.005   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3699)
  covalent geometry    : angle       0.94135 ( 5044)
  hydrogen bonds       : bond        0.03184 (   78)
  hydrogen bonds       : angle       6.66022 (  264)
  metal coordination   : bond        0.00121 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 896.49 seconds
wall clock time: 16 minutes 12.09 seconds (972.09 seconds total)