Starting phenix.real_space_refine
on Thu Sep 18 06:25:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xkx_38430/09_2025/8xkx_38430.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4810      2.51       5
     N    1262      2.21       5
     O    1424      1.98       5
     H    7340      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14858
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 784
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "C"
      Number of atoms: 637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 637
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
    Chain: "D"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 540
          Classifications: {'peptide': 35}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 816
          Classifications: {'peptide': 50}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "A"
      Number of atoms: 4652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 4652
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 9, 'TRANS': 297}
          Chain breaks: 1
  Restraints were copied for chains:
    G, H, I, J, F
  Time building chain proxies: 4.88, per 1000 atoms: 0.33
  Number of scatterers: 14858
  At special positions: 0
  Unit cell: (136.74, 113.42, 97.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    1424      8.00
     N    1262      7.00
     C    4810      6.00
     H    7340      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 435.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1792

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      37.1% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 86 through 135
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'C' and resid 14 through 49
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'D' and resid 30 through 51
      removed outlier: 3.805A  pdb=" N   THR D  34 " --> pdb=" O   SER D  30 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 58
      removed outlier: 4.044A  pdb=" N   ASP D  55 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 12 through 44
      removed outlier: 3.778A  pdb=" N   TYR E  30 " --> pdb=" O   ASN E  26 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE E  33 " --> pdb=" O   HIS E  29 " (cutoff:3.500A)
      Proline residue:  E  34  - end of helix
    Processing helix  chain 'E' and resid 49 through 55
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.650A  pdb=" N   SER A  54 " --> pdb=" O   HIS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 364 through 373
    Processing helix  chain 'G' and resid 87 through 135
      Proline residue:  G 112  - end of helix
    Processing helix  chain 'H' and resid 14 through 49
      Proline residue:  H  39  - end of helix
    Processing helix  chain 'I' and resid 30 through 51
      removed outlier: 3.805A  pdb=" N   THR I  34 " --> pdb=" O   SER I  30 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ILE I  35 " --> pdb=" O   PRO I  31 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 51 through 58
      removed outlier: 4.044A  pdb=" N   ASP I  55 " --> pdb=" O   SER I  51 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 12 through 44
      removed outlier: 3.778A  pdb=" N   TYR J  30 " --> pdb=" O   ASN J  26 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE J  33 " --> pdb=" O   HIS J  29 " (cutoff:3.500A)
      Proline residue:  J  34  - end of helix
    Processing helix  chain 'J' and resid 49 through 55
    Processing helix  chain 'F' and resid 49 through 54
      removed outlier: 3.650A  pdb=" N   SER F  54 " --> pdb=" O   HIS F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 72
    Processing helix  chain 'F' and resid 364 through 373
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355
      removed outlier: 6.851A  pdb=" N   LEU A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 195 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   THR A 194 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   CYS A 165 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER A 136 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 115 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 351 through 355
      removed outlier: 6.851A  pdb=" N   LEU F 209 " --> pdb=" O   VAL F 205 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY F 195 " --> pdb=" O   ARG F 219 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   THR F 194 " --> pdb=" O   PRO F 185 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   CYS F 165 " --> pdb=" O   ASN F 184 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER F 136 " --> pdb=" O   ASP F 132 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA F 115 " --> pdb=" O   THR F 103 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE F  98 " --> pdb=" O   PHE F  92 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE F  92 " --> pdb=" O   PHE F  98 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1473 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: 3.93

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        0.84 -     5.73: 14986
        5.73 -    10.62: 30
       10.62 -    15.51: 0
       15.51 -    20.40: 2
       20.40 -    25.29: 2
  Warning: extremely large bond lengths.
  Bond restraints: 15020
  Sorted by residual:
  bond pdb=" CG  GLN F  99 "
       pdb=" HG1 GLN F  99 "
    ideal  model  delta    sigma   weight residual
    0.970 25.289 -24.319 2.00e-02 2.50e+03 1.48e+06
  bond pdb=" CG  GLN A  99 "
       pdb=" HG1 GLN A  99 "
    ideal  model  delta    sigma   weight residual
    0.970 25.289 -24.319 2.00e-02 2.50e+03 1.48e+06
  bond pdb=" CB  MET I  54 "
       pdb=" HB1 MET I  54 "
    ideal  model  delta    sigma   weight residual
    0.970 16.180 -15.210 2.00e-02 2.50e+03 5.78e+05
  bond pdb=" CB  MET D  54 "
       pdb=" HB1 MET D  54 "
    ideal  model  delta    sigma   weight residual
    0.970 16.180 -15.210 2.00e-02 2.50e+03 5.78e+05
  bond pdb=" CB  LEU I  53 "
       pdb=" HB1 LEU I  53 "
    ideal  model  delta    sigma   weight residual
    0.970  9.599 -8.629 2.00e-02 2.50e+03 1.86e+05
  ... (remaining 15015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    20.32: 26854
       20.32 -    40.65: 122
       40.65 -    60.97: 24
       60.97 -    81.29: 12
       81.29 -   101.62: 10
  Bond angle restraints: 27022
  Sorted by residual:
  angle pdb=" HB1 ARG C  15 "
        pdb=" CB  ARG C  15 "
        pdb=" HB2 ARG C  15 "
      ideal   model   delta    sigma   weight residual
     110.00    8.38  101.62 3.00e+00 1.11e-01 1.15e+03
  angle pdb=" HB1 ARG H  15 "
        pdb=" CB  ARG H  15 "
        pdb=" HB2 ARG H  15 "
      ideal   model   delta    sigma   weight residual
     110.00    8.39  101.61 3.00e+00 1.11e-01 1.15e+03
  angle pdb=" HG1 GLU H  13 "
        pdb=" CG  GLU H  13 "
        pdb=" HG2 GLU H  13 "
      ideal   model   delta    sigma   weight residual
     110.00   15.74   94.26 3.00e+00 1.11e-01 9.87e+02
  angle pdb=" HG1 GLU C  13 "
        pdb=" CG  GLU C  13 "
        pdb=" HG2 GLU C  13 "
      ideal   model   delta    sigma   weight residual
     110.00   15.75   94.25 3.00e+00 1.11e-01 9.87e+02
  angle pdb=" HB1 ASP F 132 "
        pdb=" CB  ASP F 132 "
        pdb=" HB2 ASP F 132 "
      ideal   model   delta    sigma   weight residual
     110.00   17.00   93.00 3.00e+00 1.11e-01 9.61e+02
  ... (remaining 27017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6331
       17.98 -    35.96: 609
       35.96 -    53.95: 146
       53.95 -    71.93: 28
       71.93 -    89.91: 8
  Dihedral angle restraints: 7122
    sinusoidal: 3802
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" C   ILE F 256 "
           pdb=" N   ILE F 256 "
           pdb=" CA  ILE F 256 "
           pdb=" CB  ILE F 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.43    9.43     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" C   ILE A 256 "
           pdb=" N   ILE A 256 "
           pdb=" CA  ILE A 256 "
           pdb=" CB  ILE A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.40    9.40     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" C   LEU H  35 "
           pdb=" N   LEU H  35 "
           pdb=" CA  LEU H  35 "
           pdb=" CB  LEU H  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.99    9.39     0      2.50e+00 1.60e-01 1.41e+01
  ... (remaining 7119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1058
       0.074 -    0.148: 96
       0.148 -    0.221: 2
       0.221 -    0.295: 2
       0.295 -    0.369: 16
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  GLN F  53 "
            pdb=" N   GLN F  53 "
            pdb=" C   GLN F  53 "
            pdb=" CB  GLN F  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CA  HIS F  49 "
            pdb=" N   HIS F  49 "
            pdb=" C   HIS F  49 "
            pdb=" CB  HIS F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" CA  SER F 158 "
            pdb=" N   SER F 158 "
            pdb=" C   SER F 158 "
            pdb=" CB  SER F 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.36e+00
  ... (remaining 1171 not shown)

  Planarity restraints: 2234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  99 "   -0.055 2.00e-02 2.50e+03   5.63e-02 4.75e+01
        pdb=" CD  GLN A  99 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  99 "    0.050 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  99 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A  99 "   -0.083 2.00e-02 2.50e+03
        pdb="HE22 GLN A  99 "    0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN F  99 "   -0.054 2.00e-02 2.50e+03   5.63e-02 4.75e+01
        pdb=" CD  GLN F  99 "    0.006 2.00e-02 2.50e+03
        pdb=" OE1 GLN F  99 "    0.050 2.00e-02 2.50e+03
        pdb=" NE2 GLN F  99 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN F  99 "   -0.083 2.00e-02 2.50e+03
        pdb="HE22 GLN F  99 "    0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN F 154 "   -0.048 2.00e-02 2.50e+03   5.49e-02 4.52e+01
        pdb=" CG  ASN F 154 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN F 154 "    0.055 2.00e-02 2.50e+03
        pdb=" ND2 ASN F 154 "   -0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN F 154 "    0.081 2.00e-02 2.50e+03
        pdb="HD22 ASN F 154 "   -0.079 2.00e-02 2.50e+03
  ... (remaining 2231 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 711
        2.18 -     2.79: 28575
        2.79 -     3.39: 39555
        3.39 -     4.00: 49834
        4.00 -     4.60: 76046
  Nonbonded interactions: 194721
  Sorted by model distance:
  nonbonded pdb=" H   ASP F 345 "
            pdb=" HA  ASP F 345 "
     model   vdw
     1.576 1.816
  nonbonded pdb=" H   ASP A 345 "
            pdb=" HA  ASP A 345 "
     model   vdw
     1.577 1.816
  nonbonded pdb=" HA  LEU D  37 "
            pdb=" HB3 LEU D  37 "
     model   vdw
     1.592 1.952
  nonbonded pdb=" HA  LEU I  37 "
            pdb=" HB3 LEU I  37 "
     model   vdw
     1.592 1.952
  nonbonded pdb=" H   ILE A 256 "
            pdb=" HA  ILE A 256 "
     model   vdw
     1.594 1.816
  ... (remaining 194716 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.880
  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:             0.090
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.060
  Find NCS groups from input model:        0.090
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
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      :  0.004   0.046   7680  Z= 0.246
  Angle     :  0.741   9.069  10412  Z= 0.471
  Chirality :  0.058   0.369   1174
  Planarity :  0.004   0.049   1332
  Dihedral  : 16.096  89.910   2750
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 25.98 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.29), residues: 934
  helix:  3.12 (0.27), residues: 344
  sheet: -0.01 (0.26), residues: 390
  loop : -0.76 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  52 
 TYR   0.021   0.001   TYR F 171 
 PHE   0.008   0.001   PHE F 359 
 TRP   0.008   0.001   TRP J  32 
 HIS   0.007   0.001   HIS H  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 7680)
  covalent geometry    : angle       0.74123 (10412)
  hydrogen bonds       : bond        0.17431 (  509)
  hydrogen bonds       : angle       8.08661 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 190
  average time/residue: 0.1699
  time to fit residues: 45.4097
Evaluate side-chains
  176 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 174
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain F residue  261 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 252 ASN
** F 364 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.176712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.125295 restraints weight = 23547.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.129475 restraints weight = 14768.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132151 restraints weight = 11241.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.133430 restraints weight = 9596.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.134712 restraints weight = 8805.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7680  Z= 0.239
  Angle     :  0.687   9.573  10412  Z= 0.370
  Chirality :  0.059   0.446   1174
  Planarity :  0.004   0.040   1332
  Dihedral  :  4.895  51.270   1014
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 25.00 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.29), residues: 934
  helix:  3.12 (0.27), residues: 344
  sheet: -0.19 (0.26), residues: 390
  loop : -0.77 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 310 
 TYR   0.005   0.001   TYR A 217 
 PHE   0.014   0.002   PHE A 126 
 TRP   0.005   0.001   TRP E  32 
 HIS   0.003   0.001   HIS H  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 7680)
  covalent geometry    : angle       0.68703 (10412)
  hydrogen bonds       : bond        0.04154 (  509)
  hydrogen bonds       : angle       6.00170 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6588 (mpt90)
REVERT: A  345 ASP cc_start: 0.7951 (t0) cc_final: 0.7461 (t0)
REVERT: H   15 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6540 (mpt90)
REVERT: F  345 ASP cc_start: 0.7942 (t0) cc_final: 0.7612 (t0)
  outliers start: 32
  outliers final: 20
  residues processed: 201
  average time/residue: 0.1709
  time to fit residues: 48.1125
Evaluate side-chains
  193 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain E residue   45 SER
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain H residue   13 GLU
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain J residue   45 SER
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  132 ASP
Chi-restraints excluded: chain F residue  180 VAL
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0270
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.2044

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 252 ASN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.181020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129064 restraints weight = 23372.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.133472 restraints weight = 14349.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.136337 restraints weight = 10817.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.137656 restraints weight = 9189.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.138870 restraints weight = 8425.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7680  Z= 0.169
  Angle     :  0.603   9.207  10412  Z= 0.323
  Chirality :  0.058   0.434   1174
  Planarity :  0.003   0.041   1332
  Dihedral  :  4.814  50.441   1014
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 26.34 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.29), residues: 934
  helix:  3.16 (0.27), residues: 344
  sheet: -0.36 (0.26), residues: 388
  loop : -0.91 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.005   0.001   TYR F 114 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.005   0.001   TRP J  32 
 HIS   0.005   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7680)
  covalent geometry    : angle       0.60319 (10412)
  hydrogen bonds       : bond        0.03044 (  509)
  hydrogen bonds       : angle       5.37669 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.7933 (t0) cc_final: 0.7624 (t0)
REVERT: F  345 ASP cc_start: 0.7956 (t0) cc_final: 0.7665 (t0)
  outliers start: 18
  outliers final: 18
  residues processed: 179
  average time/residue: 0.1707
  time to fit residues: 42.6000
Evaluate side-chains
  180 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0980
   chunk 84 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 HIS
** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.181406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130834 restraints weight = 23192.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.134796 restraints weight = 14045.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.135606 restraints weight = 10116.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.136679 restraints weight = 9774.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136771 restraints weight = 9138.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7680  Z= 0.133
  Angle     :  0.575   9.150  10412  Z= 0.306
  Chirality :  0.057   0.430   1174
  Planarity :  0.003   0.040   1332
  Dihedral  :  4.654  47.388   1014
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 26.34 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.29), residues: 934
  helix:  3.24 (0.27), residues: 344
  sheet: -0.40 (0.26), residues: 388
  loop : -0.92 (0.45), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.007   0.001   TYR A 217 
 PHE   0.016   0.001   PHE A 359 
 TRP   0.005   0.001   TRP F 260 
 HIS   0.003   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7680)
  covalent geometry    : angle       0.57492 (10412)
  hydrogen bonds       : bond        0.02701 (  509)
  hydrogen bonds       : angle       5.06925 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  126 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7667 (ttm)
REVERT: A   94 MET cc_start: 0.8013 (tpp) cc_final: 0.7704 (tpp)
  outliers start: 19
  outliers final: 18
  residues processed: 182
  average time/residue: 0.1756
  time to fit residues: 44.3025
Evaluate side-chains
  182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.179397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127051 restraints weight = 23368.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131463 restraints weight = 14450.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134337 restraints weight = 10862.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.135705 restraints weight = 9229.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.137073 restraints weight = 8454.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7680  Z= 0.166
  Angle     :  0.578   9.108  10412  Z= 0.308
  Chirality :  0.057   0.430   1174
  Planarity :  0.003   0.039   1332
  Dihedral  :  4.654  46.612   1014
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.34 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.29), residues: 934
  helix:  3.29 (0.27), residues: 344
  sheet: -0.54 (0.26), residues: 390
  loop : -0.93 (0.47), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.005   0.001   TYR A 114 
 PHE   0.015   0.001   PHE B  87 
 TRP   0.006   0.001   TRP A 260 
 HIS   0.008   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7680)
  covalent geometry    : angle       0.57786 (10412)
  hydrogen bonds       : bond        0.02597 (  509)
  hydrogen bonds       : angle       4.89780 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.7845 (tpp) cc_final: 0.7488 (tpp)
REVERT: F   94 MET cc_start: 0.7832 (tpp) cc_final: 0.7457 (tpp)
REVERT: F  345 ASP cc_start: 0.7918 (t0) cc_final: 0.7635 (t0)
  outliers start: 23
  outliers final: 20
  residues processed: 184
  average time/residue: 0.1724
  time to fit residues: 44.5249
Evaluate side-chains
  185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 HIS
** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.179978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126938 restraints weight = 23358.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.131421 restraints weight = 14531.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134327 restraints weight = 10973.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135752 restraints weight = 9349.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137074 restraints weight = 8583.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7680  Z= 0.146
  Angle     :  0.571   9.281  10412  Z= 0.304
  Chirality :  0.057   0.433   1174
  Planarity :  0.003   0.037   1332
  Dihedral  :  4.577  45.320   1014
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.73 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.29), residues: 934
  helix:  3.30 (0.27), residues: 344
  sheet: -0.51 (0.27), residues: 390
  loop : -0.92 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 310 
 TYR   0.005   0.001   TYR F 114 
 PHE   0.011   0.001   PHE E  35 
 TRP   0.006   0.001   TRP A 260 
 HIS   0.010   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7680)
  covalent geometry    : angle       0.57100 (10412)
  hydrogen bonds       : bond        0.02500 (  509)
  hydrogen bonds       : angle       4.78899 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 164
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.7809 (tpp) cc_final: 0.7457 (tpp)
  outliers start: 30
  outliers final: 26
  residues processed: 185
  average time/residue: 0.1712
  time to fit residues: 44.3852
Evaluate side-chains
  188 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  108 SER
Chi-restraints excluded: chain F residue  136 SER
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.180639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129790 restraints weight = 22968.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.133812 restraints weight = 14663.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136480 restraints weight = 11300.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.137868 restraints weight = 9712.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.139042 restraints weight = 8921.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7680  Z= 0.124
  Angle     :  0.561   9.244  10412  Z= 0.298
  Chirality :  0.057   0.431   1174
  Planarity :  0.003   0.035   1332
  Dihedral  :  4.475  42.769   1014
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.85 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.30), residues: 934
  helix:  3.34 (0.27), residues: 344
  sheet: -0.43 (0.27), residues: 388
  loop : -0.89 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.004   0.001   TYR A 114 
 PHE   0.016   0.001   PHE J  35 
 TRP   0.007   0.001   TRP J  32 
 HIS   0.012   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7680)
  covalent geometry    : angle       0.56083 (10412)
  hydrogen bonds       : bond        0.02439 (  509)
  hydrogen bonds       : angle       4.69224 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 23
  residues processed: 183
  average time/residue: 0.1681
  time to fit residues: 43.0248
Evaluate side-chains
  183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  108 SER
Chi-restraints excluded: chain F residue  136 SER
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 8 optimal weight:    0.1980
   chunk 78 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 HIS
** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.178283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125350 restraints weight = 23440.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129658 restraints weight = 14657.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.132488 restraints weight = 11145.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133938 restraints weight = 9513.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.135194 restraints weight = 8710.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7680  Z= 0.205
  Angle     :  0.589   9.362  10412  Z= 0.315
  Chirality :  0.058   0.436   1174
  Planarity :  0.003   0.035   1332
  Dihedral  :  4.591  45.040   1014
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 24.63 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.30), residues: 934
  helix:  3.34 (0.27), residues: 344
  sheet: -0.51 (0.27), residues: 388
  loop : -0.96 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 315 
 TYR   0.006   0.001   TYR A 114 
 PHE   0.012   0.002   PHE A 126 
 TRP   0.007   0.001   TRP E  32 
 HIS   0.011   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7680)
  covalent geometry    : angle       0.58914 (10412)
  hydrogen bonds       : bond        0.02536 (  509)
  hydrogen bonds       : angle       4.69639 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 ASP cc_start: 0.7900 (t0) cc_final: 0.7648 (t0)
REVERT: F  345 ASP cc_start: 0.7921 (t0) cc_final: 0.7658 (t0)
  outliers start: 38
  outliers final: 32
  residues processed: 194
  average time/residue: 0.1724
  time to fit residues: 47.0362
Evaluate side-chains
  197 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  261 ARG
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain J residue   27 VAL
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  108 SER
Chi-restraints excluded: chain F residue  136 SER
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  261 ARG
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  351 THR
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** E  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.180059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.127307 restraints weight = 23366.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131815 restraints weight = 14317.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.134766 restraints weight = 10813.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.136550 restraints weight = 9168.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137332 restraints weight = 8363.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7680  Z= 0.125
  Angle     :  0.565   9.293  10412  Z= 0.301
  Chirality :  0.057   0.430   1174
  Planarity :  0.003   0.034   1332
  Dihedral  :  4.506  42.977   1014
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 26.10 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.30), residues: 934
  helix:  3.39 (0.27), residues: 344
  sheet: -0.49 (0.27), residues: 388
  loop : -0.91 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 310 
 TYR   0.007   0.001   TYR J  38 
 PHE   0.010   0.001   PHE A 116 
 TRP   0.007   0.001   TRP J  32 
 HIS   0.012   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7680)
  covalent geometry    : angle       0.56460 (10412)
  hydrogen bonds       : bond        0.02433 (  509)
  hydrogen bonds       : angle       4.60830 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 21
  residues processed: 178
  average time/residue: 0.1687
  time to fit residues: 42.2880
Evaluate side-chains
  181 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  108 SER
Chi-restraints excluded: chain F residue  136 SER
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** 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 = 0.4184 r_free = 0.4184 target = 0.180076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127232 restraints weight = 23336.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131759 restraints weight = 14320.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134695 restraints weight = 10789.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.136379 restraints weight = 9177.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.136955 restraints weight = 8377.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7680  Z= 0.124
  Angle     :  0.561   9.244  10412  Z= 0.298
  Chirality :  0.057   0.430   1174
  Planarity :  0.003   0.034   1332
  Dihedral  :  4.233  40.169   1006
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.46 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.30), residues: 934
  helix:  3.41 (0.27), residues: 344
  sheet: -0.49 (0.27), residues: 388
  loop : -0.84 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 310 
 TYR   0.005   0.001   TYR A 307 
 PHE   0.011   0.001   PHE J  35 
 TRP   0.009   0.001   TRP J  32 
 HIS   0.012   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7680)
  covalent geometry    : angle       0.56079 (10412)
  hydrogen bonds       : bond        0.02355 (  509)
  hydrogen bonds       : angle       4.52416 ( 1473)

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 22
  residues processed: 180
  average time/residue: 0.1670
  time to fit residues: 42.5219
Evaluate side-chains
  183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain C residue   15 ARG
Chi-restraints excluded: chain C residue   17 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain G residue   95 SER
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain H residue   15 ARG
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  108 SER
Chi-restraints excluded: chain F residue  136 SER
Chi-restraints excluded: chain F residue  150 ILE
Chi-restraints excluded: chain F residue  182 THR
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  268 GLU
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 364 ASN ** 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 = 0.4182 r_free = 0.4182 target = 0.179876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.127444 restraints weight = 23070.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131829 restraints weight = 14376.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134698 restraints weight = 10851.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136084 restraints weight = 9220.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.137354 restraints weight = 8460.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7680  Z= 0.222
  Angle     :  0.599   9.388  10412  Z= 0.320
  Chirality :  0.058   0.437   1174
  Planarity :  0.003   0.034   1332
  Dihedral  :  4.437  43.260   1006
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 25.98 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.30), residues: 934
  helix:  3.34 (0.27), residues: 344
  sheet: -0.55 (0.27), residues: 388
  loop : -0.92 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 315 
 TYR   0.009   0.001   TYR J  38 
 PHE   0.014   0.002   PHE A 126 
 TRP   0.009   0.001   TRP E  32 
 HIS   0.013   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 7680)
  covalent geometry    : angle       0.59887 (10412)
  hydrogen bonds       : bond        0.02539 (  509)
  hydrogen bonds       : angle       4.59744 ( 1473)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3007.94 seconds
wall clock time: 51 minutes 59.22 seconds (3119.22 seconds total)