Starting phenix.real_space_refine
on Mon Jan 13 19:14:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b34_44125/01_2025/9b34_44125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b34_44125/01_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_44125/01_2025/9b34_44125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b34_44125/01_2025/9b34_44125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b34_44125/01_2025/9b34_44125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b34_44125/01_2025/9b34_44125.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 2.90, per 1000 atoms: 0.80
  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: 0.94
  Conformation dependent library (CDL) restraints added in 419.2 milliseconds
  
  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: 0.54
  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: 0.88

  Time building geometry restraints manager: 1.04 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 237 or resid 1001 th \ 
rough 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:             0.710
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.540
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
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   3699  Z= 0.407
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.035   0.005   TRP E 182 
 HIS   0.004   0.001   HIS E  51 
 PHE   0.036   0.005   PHE E 130 
 TYR   0.016   0.003   TYR E 176 
 ARG   0.009   0.002   ARG F 228 

*********************** 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  : 0.395 
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: 0.1821
  time to fit residues: 30.4363
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  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0470
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.4310 r_free = 0.4310 target = 0.165301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.148382 restraints weight = 6205.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.152794 restraints weight = 3457.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.155708 restraints weight = 2249.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3699  Z= 0.222
  Angle     :  1.024  19.053   5044  Z= 0.520
  Chirality :  0.054   0.194    580
  Planarity :  0.007   0.052    651
  Dihedral  : 10.769  51.545    500
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 21.49 %
    Favored  : 77.23 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.47 (0.33), residues: 470
  helix:  None (None), residues: 0
  sheet: -4.06 (0.36), residues: 156
  loop : -3.59 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP E 182 
 HIS   0.006   0.001   HIS E 121 
 PHE   0.018   0.002   PHE F 128 
 TYR   0.016   0.002   TYR E  12 
 ARG   0.004   0.001   ARG F  90 

*********************** 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
  103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 ILE cc_start: 0.7983 (pp) cc_final: 0.7765 (mt)
REVERT: E  129 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6698 (ttp)
REVERT: E  158 ARG cc_start: 0.6128 (mtp-110) cc_final: 0.5764 (mmm-85)
REVERT: E  228 ARG cc_start: 0.7062 (ptp-110) cc_final: 0.5253 (mpt180)
REVERT: E  229 LEU cc_start: 0.8192 (mt) cc_final: 0.7985 (mt)
REVERT: F   54 TYR cc_start: 0.7227 (t80) cc_final: 0.6752 (t80)
REVERT: F  126 LEU cc_start: 0.8515 (tp) cc_final: 0.8224 (tp)
  outliers start: 11
  outliers final: 4
  residues processed: 97
  average time/residue: 0.1745
  time to fit residues: 21.0652
Evaluate side-chains
  78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  223 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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  51 HIS
F 180 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.121609 restraints weight = 6290.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.125194 restraints weight = 3827.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127620 restraints weight = 2637.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   3699  Z= 0.379
  Angle     :  1.043  16.980   5044  Z= 0.537
  Chirality :  0.055   0.200    580
  Planarity :  0.007   0.045    651
  Dihedral  : 10.891  57.975    500
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 22.17
  Ramachandran Plot:
    Outliers :  1.49 %
    Allowed  : 24.04 %
    Favored  : 74.47 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 15.80 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.33 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.22 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.30 (0.36), residues: 170
  loop : -3.76 (0.31), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP E 109 
 HIS   0.012   0.003   HIS F 180 
 PHE   0.021   0.003   PHE E 191 
 TYR   0.033   0.003   TYR F  12 
 ARG   0.008   0.001   ARG F 228 

*********************** 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
  108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  129 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6713 (ttt)
REVERT: E  158 ARG cc_start: 0.6085 (mtp-110) cc_final: 0.5701 (mmm-85)
REVERT: E  228 ARG cc_start: 0.7622 (ptp-110) cc_final: 0.5655 (mpt180)
REVERT: F   54 TYR cc_start: 0.7718 (t80) cc_final: 0.7497 (t80)
REVERT: F   94 SER cc_start: 0.8634 (t) cc_final: 0.7895 (p)
REVERT: F  141 ILE cc_start: 0.7928 (mt) cc_final: 0.7727 (mp)
REVERT: F  145 ASP cc_start: 0.7361 (m-30) cc_final: 0.7012 (t0)
REVERT: F  159 VAL cc_start: 0.6784 (p) cc_final: 0.6113 (m)
  outliers start: 22
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1454
  time to fit residues: 17.2455
Evaluate side-chains
  86 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  129 MET
Chi-restraints excluded: chain E residue  179 VAL
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   27 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   81 LEU
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  180 HIS
Chi-restraints excluded: chain F residue  220 SER
Chi-restraints excluded: chain F residue  223 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0030
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
E 131 ASN
F 180 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.145218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.127232 restraints weight = 6123.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.130905 restraints weight = 3708.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.133433 restraints weight = 2553.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3699  Z= 0.224
  Angle     :  0.947  17.567   5044  Z= 0.479
  Chirality :  0.051   0.186    580
  Planarity :  0.006   0.040    651
  Dihedral  : 10.265  51.750    500
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 22.77 %
    Favored  : 75.96 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 20.00 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.87 (0.34), residues: 470
  helix:  None (None), residues: 0
  sheet: -3.08 (0.43), residues: 134
  loop : -3.56 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 182 
 HIS   0.011   0.002   HIS F 180 
 PHE   0.016   0.002   PHE E 128 
 TYR   0.012   0.001   TYR F  12 
 ARG   0.003   0.001   ARG E  90 

*********************** 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
  95 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  126 LEU cc_start: 0.8963 (tp) cc_final: 0.8760 (tp)
REVERT: E  129 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6680 (ttt)
REVERT: E  158 ARG cc_start: 0.6173 (mtp-110) cc_final: 0.5749 (mmm-85)
REVERT: F   94 SER cc_start: 0.8451 (t) cc_final: 0.7788 (p)
REVERT: F  145 ASP cc_start: 0.7265 (m-30) cc_final: 0.6910 (t0)
REVERT: F  208 ASP cc_start: 0.5384 (t0) cc_final: 0.4955 (m-30)
  outliers start: 21
  outliers final: 13
  residues processed: 86
  average time/residue: 0.1259
  time to fit residues: 14.0749
Evaluate side-chains
  86 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
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   91 VAL
Chi-restraints excluded: chain E residue  129 MET
Chi-restraints excluded: chain E residue  179 VAL
Chi-restraints excluded: chain E residue  210 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  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
Chi-restraints excluded: chain F residue  232 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0050
   chunk 35 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
E 180 HIS
F 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.144773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126925 restraints weight = 6292.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.130494 restraints weight = 3789.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133065 restraints weight = 2629.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.6067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3699  Z= 0.282
  Angle     :  0.971  17.656   5044  Z= 0.493
  Chirality :  0.054   0.201    580
  Planarity :  0.006   0.038    651
  Dihedral  : 10.269  48.276    500
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 24.68 %
    Favored  : 74.26 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 19.01 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.77 (0.35), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.94 (0.42), residues: 142
  loop : -3.51 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP E 182 
 HIS   0.007   0.001   HIS E 121 
 PHE   0.023   0.002   PHE E 191 
 TYR   0.023   0.002   TYR F  12 
 ARG   0.008   0.001   ARG F  33 

*********************** 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
  108 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  129 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6941 (ttt)
REVERT: F   93 LEU cc_start: 0.8811 (mp) cc_final: 0.8602 (mm)
REVERT: F   94 SER cc_start: 0.8438 (t) cc_final: 0.7664 (p)
REVERT: F  145 ASP cc_start: 0.7399 (m-30) cc_final: 0.6954 (t0)
REVERT: F  208 ASP cc_start: 0.5851 (t0) cc_final: 0.5523 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 96
  average time/residue: 0.1299
  time to fit residues: 15.7955
Evaluate side-chains
  94 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   49 THR
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  129 MET
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 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   64 VAL
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0870
   overall best weight:    1.3162

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.142693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124731 restraints weight = 6311.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.128346 restraints weight = 3786.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.130855 restraints weight = 2595.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.6612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3699  Z= 0.295
  Angle     :  0.969  16.107   5044  Z= 0.492
  Chirality :  0.054   0.194    580
  Planarity :  0.006   0.044    651
  Dihedral  : 10.205  48.700    500
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 20.91
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  : 24.04 %
    Favored  : 74.68 %
  Rotamer:
    Outliers :  8.64 %
    Allowed  : 18.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.73 (0.35), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.85 (0.43), residues: 136
  loop : -3.53 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP E 182 
 HIS   0.008   0.001   HIS E 121 
 PHE   0.016   0.002   PHE E 128 
 TYR   0.018   0.002   TYR F  12 
 ARG   0.008   0.001   ARG F  33 

*********************** 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
  107 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6083 (t70)
REVERT: E  232 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7768 (pp)
REVERT: F   93 LEU cc_start: 0.8805 (mp) cc_final: 0.8546 (mm)
REVERT: F   94 SER cc_start: 0.8447 (t) cc_final: 0.7850 (p)
REVERT: F  145 ASP cc_start: 0.7427 (m-30) cc_final: 0.6936 (t0)
REVERT: F  208 ASP cc_start: 0.6164 (t0) cc_final: 0.5914 (m-30)
REVERT: F  223 SER cc_start: 0.7215 (OUTLIER) cc_final: 0.6911 (t)
  outliers start: 35
  outliers final: 24
  residues processed: 91
  average time/residue: 0.1389
  time to fit residues: 16.0424
Evaluate side-chains
  96 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   28 ASP
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue   91 VAL
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 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   27 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   81 LEU
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain F residue  110 SER
Chi-restraints excluded: chain F residue  166 GLN
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  210 ILE
Chi-restraints excluded: chain F residue  218 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    0.0070
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.143744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.126089 restraints weight = 6244.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.129671 restraints weight = 3699.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.132081 restraints weight = 2538.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.6804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3699  Z= 0.204
  Angle     :  0.921  14.898   5044  Z= 0.465
  Chirality :  0.051   0.172    580
  Planarity :  0.006   0.041    651
  Dihedral  :  9.704  46.713    500
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 22.13 %
    Favored  : 76.81 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 21.48 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.35), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.65 (0.44), residues: 140
  loop : -3.42 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP E 182 
 HIS   0.006   0.001   HIS E 121 
 PHE   0.027   0.002   PHE E 191 
 TYR   0.008   0.001   TYR F  54 
 ARG   0.006   0.001   ARG F  33 

*********************** 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: 25
    poor density    : 76
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.5955 (t70)
REVERT: E  232 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7781 (pp)
REVERT: F   59 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7996 (tppt)
REVERT: F   94 SER cc_start: 0.8385 (t) cc_final: 0.7974 (p)
REVERT: F  145 ASP cc_start: 0.7042 (m-30) cc_final: 0.6707 (t0)
REVERT: F  208 ASP cc_start: 0.6061 (t0) cc_final: 0.5599 (m-30)
REVERT: F  223 SER cc_start: 0.6973 (OUTLIER) cc_final: 0.6637 (t)
  outliers start: 25
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1399
  time to fit residues: 16.2351
Evaluate side-chains
  90 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   91 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 E residue  232 LEU
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  176 TYR
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  210 ILE
Chi-restraints excluded: chain F residue  218 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.146942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.129325 restraints weight = 6144.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.132901 restraints weight = 3644.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.135420 restraints weight = 2498.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.7204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3699  Z= 0.192
  Angle     :  0.921  14.196   5044  Z= 0.460
  Chirality :  0.051   0.236    580
  Planarity :  0.005   0.041    651
  Dihedral  :  9.352  45.396    500
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 22.98 %
    Favored  : 76.17 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 24.20 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.57 (0.44), residues: 144
  loop : -3.34 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP E 182 
 HIS   0.005   0.001   HIS E 121 
 PHE   0.015   0.002   PHE F 191 
 TYR   0.009   0.001   TYR F  12 
 ARG   0.005   0.001   ARG F  33 

*********************** 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
  93 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.5837 (t70)
REVERT: F   94 SER cc_start: 0.8391 (t) cc_final: 0.8050 (p)
REVERT: F  145 ASP cc_start: 0.6833 (m-30) cc_final: 0.6562 (t0)
REVERT: F  208 ASP cc_start: 0.5826 (t0) cc_final: 0.5411 (m-30)
REVERT: F  223 SER cc_start: 0.7254 (OUTLIER) cc_final: 0.6814 (t)
  outliers start: 20
  outliers final: 13
  residues processed: 86
  average time/residue: 0.1441
  time to fit residues: 15.7177
Evaluate side-chains
  77 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  142 LEU
Chi-restraints excluded: chain F residue  218 ASP
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 39 optimal weight:    0.0670
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0060
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5134

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

Flipped N/Q/H residues before XYZ refinement:
F  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.146638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.129347 restraints weight = 6058.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.132961 restraints weight = 3593.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.135434 restraints weight = 2458.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.7415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3699  Z= 0.207
  Angle     :  0.917  13.601   5044  Z= 0.458
  Chirality :  0.051   0.234    580
  Planarity :  0.005   0.039    651
  Dihedral  :  9.169  44.540    500
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 22.34 %
    Favored  : 76.81 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.42 (0.45), residues: 144
  loop : -3.33 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP E 182 
 HIS   0.005   0.001   HIS E 121 
 PHE   0.024   0.002   PHE E 191 
 TYR   0.013   0.001   TYR F  12 
 ARG   0.004   0.001   ARG F  33 

*********************** 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
  91 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.5798 (t70)
REVERT: E  213 PHE cc_start: 0.8725 (p90) cc_final: 0.8242 (p90)
REVERT: E  232 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7761 (pp)
REVERT: F   10 ASP cc_start: 0.6233 (t0) cc_final: 0.5866 (t0)
REVERT: F   94 SER cc_start: 0.8334 (t) cc_final: 0.8042 (p)
REVERT: F  208 ASP cc_start: 0.5936 (t0) cc_final: 0.5502 (m-30)
REVERT: F  223 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.6787 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1518
  time to fit residues: 16.2188
Evaluate side-chains
  78 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  142 LEU
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  218 ASP
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 36 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0010
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
E 132 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.142636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.123926 restraints weight = 6284.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.127734 restraints weight = 3760.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.130414 restraints weight = 2589.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.7676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3699  Z= 0.225
  Angle     :  0.932  13.607   5044  Z= 0.464
  Chirality :  0.052   0.222    580
  Planarity :  0.006   0.038    651
  Dihedral  :  9.134  43.897    500
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 23.62 %
    Favored  : 75.53 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 26.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.36), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.44 (0.45), residues: 144
  loop : -3.32 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP E 182 
 HIS   0.005   0.001   HIS E 121 
 PHE   0.028   0.002   PHE F 191 
 TYR   0.023   0.001   TYR F  12 
 ARG   0.007   0.001   ARG E  33 

********************** 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
  83 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   51 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.5796 (t70)
REVERT: E  130 PHE cc_start: 0.7681 (m-80) cc_final: 0.7417 (m-80)
REVERT: E  213 PHE cc_start: 0.8759 (p90) cc_final: 0.8270 (p90)
REVERT: E  232 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7788 (pp)
REVERT: F   94 SER cc_start: 0.8397 (t) cc_final: 0.8050 (p)
REVERT: F  208 ASP cc_start: 0.5850 (t0) cc_final: 0.5432 (m-30)
REVERT: F  223 SER cc_start: 0.7192 (OUTLIER) cc_final: 0.6724 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 79
  average time/residue: 0.1462
  time to fit residues: 14.5372
Evaluate side-chains
  79 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   51 HIS
Chi-restraints excluded: chain E residue   62 SER
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain F residue   25 ILE
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  179 VAL
Chi-restraints excluded: chain F residue  218 ASP
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 40 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0970
   chunk 20 optimal weight:    0.0060
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.2394

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.149078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.130728 restraints weight = 6169.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.134571 restraints weight = 3663.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.137131 restraints weight = 2514.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.7897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3699  Z= 0.196
  Angle     :  0.916  13.930   5044  Z= 0.452
  Chirality :  0.051   0.234    580
  Planarity :  0.005   0.039    651
  Dihedral  :  8.770  44.215    500
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  : 22.34 %
    Favored  : 76.81 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 27.16 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.89 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.24 (0.37), residues: 470
  helix:  None (None), residues: 0
  sheet: -2.34 (0.45), residues: 142
  loop : -3.27 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP E 182 
 HIS   0.005   0.001   HIS E 121 
 PHE   0.026   0.002   PHE E 191 
 TYR   0.011   0.001   TYR F  54 
 ARG   0.005   0.001   ARG E  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1588.67 seconds
wall clock time: 29 minutes 18.60 seconds (1758.60 seconds total)