Starting phenix.real_space_refine
on Tue Mar 11 20:49:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rle_19340/03_2025/8rle_19340.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
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      15      5.16       5
     C    2144      2.51       5
     N     605      2.21       5
     O     664      1.98       5
     H    3190      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6618
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 3262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 3262
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 10, 'TRANS': 209}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 1659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 1659
          Classifications: {'peptide': 114}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 1697
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 4.00, per 1000 atoms: 0.60
  Number of scatterers: 6618
  At special positions: 0
  Unit cell: (60.58, 86.676, 82.948, 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      15     16.00
     O     664      8.00
     N     605      7.00
     C    2144      6.00
     H    3190      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  11 " - pdb=" SG  CYS C  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 546.4 milliseconds
  

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  810

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 5 sheets defined
      9.1% alpha, 40.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'B' and resid 57 through 66
      removed outlier: 4.338A  pdb=" N   THR B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 4.532A  pdb=" N   ARG B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 90
    Processing helix  chain 'B' and resid 134 through 139
    Processing helix  chain 'D' and resid 83 through 88
      removed outlier: 3.915A  pdb=" N   ALA D  88 " --> pdb=" O   GLU D  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.544A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 22
      removed outlier: 5.619A  pdb=" N   ASN B 149 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LYS B 166 " --> pdb=" O   ASN B 149 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE B 161 " --> pdb=" O   ASN B 185 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B 119 " --> pdb=" O   PRO B  13 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B  15 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ASN B 121 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ILE B 123 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7
      removed outlier: 3.871A  pdb=" N   THR D  77 " --> pdb=" O   ASP D  72 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASP D  72 " --> pdb=" O   THR D  77 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59
      removed outlier: 6.929A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLY D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   MET D  34 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.587A  pdb=" N   THR C  77 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59
      removed outlier: 6.612A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   ASN C  50 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   THR C  34 " --> pdb=" O   ASN C  50 " (cutoff:3.500A)

    150 hydrogen bonds defined for protein.
    390 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: 2.02

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3188
        1.03 -     1.23: 4
        1.23 -     1.42: 1534
        1.42 -     1.62: 1945
        1.62 -     1.81: 22
  Bond restraints: 6693
  Sorted by residual:
  bond pdb=" N   VAL B 206 "
       pdb=" CA  VAL B 206 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.18e-02 7.18e+03 1.06e+01
  bond pdb=" N   LEU B 207 "
       pdb=" CA  LEU B 207 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.21e-02 6.83e+03 7.87e+00
  bond pdb=" N   SER B 205 "
       pdb=" CA  SER B 205 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.21e-02 6.83e+03 7.63e+00
  bond pdb=" N   SER B 208 "
       pdb=" CA  SER B 208 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.29e-02 6.01e+03 7.34e+00
  bond pdb=" N   GLN B 204 "
       pdb=" H   GLN B 204 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.84e+00
  ... (remaining 6688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 11249
        1.07 -     2.14: 671
        2.14 -     3.21: 44
        3.21 -     4.28: 17
        4.28 -     5.35: 1
  Bond angle restraints: 11982
  Sorted by residual:
  angle pdb=" CA  SER B 208 "
        pdb=" C   SER B 208 "
        pdb=" O   SER B 208 "
      ideal   model   delta    sigma   weight residual
     121.44  117.66    3.78 1.17e+00 7.31e-01 1.04e+01
  angle pdb=" CA  GLN B 204 "
        pdb=" C   GLN B 204 "
        pdb=" O   GLN B 204 "
      ideal   model   delta    sigma   weight residual
     120.40  117.10    3.30 1.05e+00 9.07e-01 9.89e+00
  angle pdb=" N   PHE B 165 "
        pdb=" CA  PHE B 165 "
        pdb=" C   PHE B 165 "
      ideal   model   delta    sigma   weight residual
     107.88  112.13   -4.25 1.41e+00 5.03e-01 9.08e+00
  angle pdb=" CA  VAL B 206 "
        pdb=" C   VAL B 206 "
        pdb=" O   VAL B 206 "
      ideal   model   delta    sigma   weight residual
     120.67  117.36    3.31 1.12e+00 7.97e-01 8.76e+00
  angle pdb=" CA  LEU B 207 "
        pdb=" C   LEU B 207 "
        pdb=" O   LEU B 207 "
      ideal   model   delta    sigma   weight residual
     120.36  117.23    3.13 1.08e+00 8.57e-01 8.42e+00
  ... (remaining 11977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 2842
       16.07 -    32.14: 265
       32.14 -    48.22: 63
       48.22 -    64.29: 32
       64.29 -    80.36: 2
  Dihedral angle restraints: 3204
    sinusoidal: 1684
      harmonic: 1520
  Sorted by residual:
  dihedral pdb=" CB  CYS D  11 "
           pdb=" SG  CYS D  11 "
           pdb=" SG  CYS C  11 "
           pdb=" CB  CYS C  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.18  -45.82     1      1.00e+01 1.00e-02 2.91e+01
  dihedral pdb=" CA  VAL B 219 "
           pdb=" C   VAL B 219 "
           pdb=" N   LEU B 220 "
           pdb=" CA  LEU B 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.43  -15.57     0      5.00e+00 4.00e-02 9.70e+00
  dihedral pdb=" CA  ASP B  76 "
           pdb=" CB  ASP B  76 "
           pdb=" CG  ASP B  76 "
           pdb=" OD1 ASP B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.85   51.85     1      2.00e+01 2.50e-03 9.17e+00
  ... (remaining 3201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 345
       0.035 -    0.071: 111
       0.071 -    0.106: 31
       0.106 -    0.142: 23
       0.142 -    0.177: 2
  Chirality restraints: 512
  Sorted by residual:
  chirality pdb=" CA  ILE B 152 "
            pdb=" N   ILE B 152 "
            pdb=" C   ILE B 152 "
            pdb=" CB  ILE B 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.84e-01
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.08e-01
  chirality pdb=" CA  LEU B 207 "
            pdb=" N   LEU B 207 "
            pdb=" C   LEU B 207 "
            pdb=" CB  LEU B 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 509 not shown)

  Planarity restraints: 1059
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 204 "    0.224 2.00e-02 2.50e+03   3.99e-01 2.39e+03
        pdb=" CD  GLN B 204 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 204 "   -0.213 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 204 "   -0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN B 204 "   -0.650 2.00e-02 2.50e+03
        pdb="HE22 GLN B 204 "    0.662 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 165 "   -0.010 2.00e-02 2.50e+03   6.68e-03 1.34e+00
        pdb=" CG  PHE B 165 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 165 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 165 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 165 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 165 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 165 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 165 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  67 "    0.005 2.00e-02 2.50e+03   6.17e-03 1.14e+00
        pdb=" CG  PHE C  67 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  67 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  67 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  67 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  67 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE C  67 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE C  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 PHE C  67 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE C  67 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE C  67 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1056 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 685
        2.23 -     2.82: 14170
        2.82 -     3.42: 16695
        3.42 -     4.01: 22815
        4.01 -     4.60: 33307
  Nonbonded interactions: 87672
  Sorted by model distance:
  nonbonded pdb="HH12 ARG C  38 "
            pdb=" OD1 ASP C  89 "
     model   vdw
     1.640 2.450
  nonbonded pdb=" OH  TYR D  59 "
            pdb=" H   ILE D  69 "
     model   vdw
     1.681 2.450
  nonbonded pdb=" OE1 GLU B 142 "
            pdb=" H   GLU B 142 "
     model   vdw
     1.749 2.450
  nonbonded pdb=" HH  TYR D  59 "
            pdb=" H   ILE D  69 "
     model   vdw
     1.749 2.100
  nonbonded pdb=" O   VAL B 171 "
            pdb=" H   GLY B 174 "
     model   vdw
     1.800 2.450
  ... (remaining 87667 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 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:             2.350
  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:             0.120
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5989
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3503  Z= 0.177
  Angle     :  0.557   5.355   4753  Z= 0.314
  Chirality :  0.045   0.177    512
  Planarity :  0.004   0.034    630
  Dihedral  : 13.168  80.362   1240
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.39), residues: 444
  helix: -0.82 (1.03), residues: 29
  sheet:  0.67 (0.39), residues: 191
  loop :  0.19 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  47 
 HIS   0.005   0.001   HIS B 217 
 PHE   0.020   0.001   PHE B 165 
 TYR   0.008   0.001   TYR B 143 
 ARG   0.004   0.001   ARG D  35 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.479 
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   44 LEU cc_start: 0.8079 (mt) cc_final: 0.7788 (mt)
REVERT: B  182 TYR cc_start: 0.7036 (t80) cc_final: 0.6566 (t80)
REVERT: C  113 THR cc_start: 0.8566 (t) cc_final: 0.7878 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.3273
  time to fit residues: 47.9683
Evaluate side-chains
  112 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
B  77 HIS
B 204 GLN
** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 ASN
C  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.161088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.138815 restraints weight = 20744.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.145042 restraints weight = 9048.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.148796 restraints weight = 4748.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3503  Z= 0.181
  Angle     :  0.544   4.714   4753  Z= 0.291
  Chirality :  0.043   0.144    512
  Planarity :  0.004   0.027    630
  Dihedral  :  4.113  13.409    493
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.58 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.39), residues: 444
  helix: -0.92 (0.97), residues: 28
  sheet:  0.67 (0.37), residues: 210
  loop :  0.19 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 217 
 PHE   0.012   0.001   PHE C  67 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.005   0.001   ARG C  98 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.481 
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   44 LEU cc_start: 0.8241 (mt) cc_final: 0.7983 (mt)
REVERT: B  182 TYR cc_start: 0.6992 (t80) cc_final: 0.6542 (t80)
REVERT: C  113 THR cc_start: 0.8260 (t) cc_final: 0.8010 (t)
  outliers start: 5
  outliers final: 2
  residues processed: 117
  average time/residue: 0.3391
  time to fit residues: 47.6478
Evaluate side-chains
  115 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   77 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
B 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.157005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.135299 restraints weight = 20690.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.141340 restraints weight = 8977.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.144912 restraints weight = 4698.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6376
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3503  Z= 0.218
  Angle     :  0.546   4.676   4753  Z= 0.294
  Chirality :  0.043   0.132    512
  Planarity :  0.004   0.038    630
  Dihedral  :  4.256  13.994    493
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.95 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.40), residues: 444
  helix: -1.78 (0.94), residues: 25
  sheet:  0.48 (0.35), residues: 231
  loop :  0.31 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 101 
 HIS   0.004   0.001   HIS B 217 
 PHE   0.021   0.002   PHE C  67 
 TYR   0.013   0.001   TYR D  91 
 ARG   0.004   0.001   ARG D  35 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.532 
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: B   44 LEU cc_start: 0.8190 (mt) cc_final: 0.7932 (mt)
REVERT: B   96 ARG cc_start: 0.6497 (mtp180) cc_final: 0.6229 (mtp180)
REVERT: B  170 ASN cc_start: 0.9125 (m110) cc_final: 0.8850 (m110)
REVERT: B  182 TYR cc_start: 0.6957 (t80) cc_final: 0.6513 (t80)
REVERT: B  218 MET cc_start: 0.8631 (mpp) cc_final: 0.8317 (mpp)
REVERT: D   35 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7220 (mtt180)
REVERT: D  106 GLN cc_start: 0.8054 (pp30) cc_final: 0.7784 (pp30)
REVERT: C  113 THR cc_start: 0.8347 (t) cc_final: 0.8123 (t)
  outliers start: 4
  outliers final: 3
  residues processed: 121
  average time/residue: 0.3510
  time to fit residues: 50.4632
Evaluate side-chains
  119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 116
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   77 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 135 ASN
C   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.154775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.132405 restraints weight = 20721.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.138492 restraints weight = 8895.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.142096 restraints weight = 4679.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3503  Z= 0.229
  Angle     :  0.557   5.010   4753  Z= 0.300
  Chirality :  0.044   0.132    512
  Planarity :  0.004   0.040    630
  Dihedral  :  4.394  15.356    493
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.95 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.40), residues: 444
  helix: -1.81 (0.95), residues: 25
  sheet:  0.58 (0.37), residues: 210
  loop :  0.04 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 101 
 HIS   0.005   0.001   HIS B 217 
 PHE   0.017   0.002   PHE C  67 
 TYR   0.013   0.002   TYR D  91 
 ARG   0.004   0.001   ARG C  39 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.487 
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: B   44 LEU cc_start: 0.8212 (mt) cc_final: 0.7939 (mt)
REVERT: B  170 ASN cc_start: 0.9177 (m110) cc_final: 0.8898 (m-40)
REVERT: B  182 TYR cc_start: 0.6974 (t80) cc_final: 0.6536 (t80)
REVERT: D  106 GLN cc_start: 0.8099 (pp30) cc_final: 0.7745 (pp30)
REVERT: C   71 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7467 (ttm110)
REVERT: C   98 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6598 (ttp80)
REVERT: C  113 THR cc_start: 0.8370 (t) cc_final: 0.8143 (t)
  outliers start: 5
  outliers final: 2
  residues processed: 116
  average time/residue: 0.3445
  time to fit residues: 47.9809
Evaluate side-chains
  115 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain D residue   77 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.153969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.132059 restraints weight = 20691.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.138068 restraints weight = 8809.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.141610 restraints weight = 4610.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3503  Z= 0.201
  Angle     :  0.544   5.650   4753  Z= 0.289
  Chirality :  0.043   0.137    512
  Planarity :  0.004   0.034    630
  Dihedral  :  4.282  14.314    493
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.36 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.41), residues: 444
  helix: -1.73 (0.97), residues: 25
  sheet:  0.54 (0.37), residues: 210
  loop : -0.00 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 109 
 HIS   0.004   0.001   HIS B 217 
 PHE   0.013   0.001   PHE C  67 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.004   0.001   ARG C  71 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  127 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.494 
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: B   44 LEU cc_start: 0.8237 (mt) cc_final: 0.7969 (mt)
REVERT: B  182 TYR cc_start: 0.6965 (t80) cc_final: 0.6534 (t80)
REVERT: D  106 GLN cc_start: 0.8066 (pp30) cc_final: 0.7651 (pp30)
REVERT: C  109 TRP cc_start: 0.8848 (m100) cc_final: 0.8516 (m100)
REVERT: C  113 THR cc_start: 0.8369 (t) cc_final: 0.8166 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 123
  average time/residue: 0.3418
  time to fit residues: 50.0448
Evaluate side-chains
  121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 MET
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
B 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.154283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.132480 restraints weight = 20671.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.138391 restraints weight = 8872.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.141980 restraints weight = 4669.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6493
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3503  Z= 0.180
  Angle     :  0.546   5.963   4753  Z= 0.288
  Chirality :  0.043   0.130    512
  Planarity :  0.005   0.059    630
  Dihedral  :  4.277  13.905    493
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.34 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.41), residues: 444
  helix: -1.66 (0.99), residues: 25
  sheet:  0.45 (0.36), residues: 216
  loop :  0.18 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 181 
 PHE   0.011   0.001   PHE C  67 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.005   0.001   ARG C  71 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 LEU cc_start: 0.8251 (mt) cc_final: 0.8011 (mt)
REVERT: B   81 HIS cc_start: 0.6858 (m90) cc_final: 0.6453 (m90)
REVERT: B  182 TYR cc_start: 0.6882 (t80) cc_final: 0.6506 (t80)
REVERT: D  106 GLN cc_start: 0.8113 (pp30) cc_final: 0.7654 (pp30)
REVERT: C  113 THR cc_start: 0.8360 (t) cc_final: 0.8159 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 120
  average time/residue: 0.3459
  time to fit residues: 49.2470
Evaluate side-chains
  120 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 41 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.153295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.131806 restraints weight = 20458.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.137673 restraints weight = 8704.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.141205 restraints weight = 4567.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3503  Z= 0.188
  Angle     :  0.548   5.722   4753  Z= 0.291
  Chirality :  0.043   0.129    512
  Planarity :  0.004   0.037    630
  Dihedral  :  4.270  13.930    493
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.49 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.41), residues: 444
  helix: -1.86 (0.96), residues: 25
  sheet:  0.50 (0.37), residues: 209
  loop :  0.01 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 181 
 PHE   0.011   0.002   PHE C  67 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.003   0.001   ARG C  71 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 LEU cc_start: 0.8248 (mt) cc_final: 0.7954 (mt)
REVERT: B   81 HIS cc_start: 0.6899 (m90) cc_final: 0.6511 (m90)
REVERT: B  182 TYR cc_start: 0.6889 (t80) cc_final: 0.6528 (t80)
REVERT: D  106 GLN cc_start: 0.8094 (pp30) cc_final: 0.7611 (pp30)
REVERT: C  113 THR cc_start: 0.8406 (t) cc_final: 0.8179 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 121
  average time/residue: 0.3135
  time to fit residues: 45.8058
Evaluate side-chains
  119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 116
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 MET
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 177 GLN
C   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.152245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.130522 restraints weight = 20456.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.136465 restraints weight = 8715.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.140026 restraints weight = 4552.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3503  Z= 0.208
  Angle     :  0.573   9.331   4753  Z= 0.302
  Chirality :  0.044   0.130    512
  Planarity :  0.005   0.056    630
  Dihedral  :  4.366  13.888    493
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.62 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.41), residues: 444
  helix: -1.31 (0.97), residues: 28
  sheet:  0.44 (0.37), residues: 209
  loop : -0.09 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 217 
 PHE   0.012   0.002   PHE C  67 
 TYR   0.019   0.002   TYR B 143 
 ARG   0.005   0.001   ARG C  39 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 LEU cc_start: 0.8223 (mt) cc_final: 0.8018 (mt)
REVERT: B   81 HIS cc_start: 0.6955 (m90) cc_final: 0.6560 (m90)
REVERT: B   96 ARG cc_start: 0.6645 (mtp-110) cc_final: 0.6374 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6900 (t80) cc_final: 0.6530 (t80)
REVERT: D    5 VAL cc_start: 0.8561 (t) cc_final: 0.8170 (p)
REVERT: D  101 TRP cc_start: 0.7935 (m100) cc_final: 0.7640 (m100)
REVERT: D  106 GLN cc_start: 0.8122 (pp30) cc_final: 0.7598 (pp30)
REVERT: C  113 THR cc_start: 0.8411 (t) cc_final: 0.8207 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 121
  average time/residue: 0.3407
  time to fit residues: 49.2689
Evaluate side-chains
  119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 MET
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain C residue  116 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   chunk 38 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.151779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.130078 restraints weight = 20539.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.136006 restraints weight = 8781.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.139547 restraints weight = 4577.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3503  Z= 0.204
  Angle     :  0.576   8.391   4753  Z= 0.304
  Chirality :  0.044   0.136    512
  Planarity :  0.004   0.044    630
  Dihedral  :  4.394  15.011    493
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.62 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.41), residues: 444
  helix: -1.33 (0.97), residues: 28
  sheet:  0.37 (0.37), residues: 215
  loop : -0.22 (0.45), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 217 
 PHE   0.012   0.002   PHE C  67 
 TYR   0.016   0.001   TYR B 143 
 ARG   0.005   0.001   ARG D  31 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 LEU cc_start: 0.8245 (mt) cc_final: 0.8004 (mt)
REVERT: B   81 HIS cc_start: 0.7025 (m90) cc_final: 0.6608 (m90)
REVERT: B   96 ARG cc_start: 0.6609 (mtp-110) cc_final: 0.6307 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6950 (t80) cc_final: 0.6577 (t80)
REVERT: D  101 TRP cc_start: 0.7958 (m100) cc_final: 0.7658 (m100)
REVERT: D  106 GLN cc_start: 0.8129 (pp30) cc_final: 0.7595 (pp30)
REVERT: C  113 THR cc_start: 0.8434 (t) cc_final: 0.8208 (t)
  outliers start: 7
  outliers final: 6
  residues processed: 119
  average time/residue: 0.3323
  time to fit residues: 47.5459
Evaluate side-chains
  121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain D residue   51 MET
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  105 THR
Chi-restraints excluded: chain C residue  116 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.151261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.128853 restraints weight = 20899.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134678 restraints weight = 9163.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.138312 restraints weight = 4935.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3503  Z= 0.187
  Angle     :  0.576   9.015   4753  Z= 0.304
  Chirality :  0.044   0.151    512
  Planarity :  0.004   0.034    630
  Dihedral  :  4.310  15.156    493
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.62 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.41), residues: 444
  helix: -1.31 (0.98), residues: 28
  sheet:  0.40 (0.37), residues: 211
  loop : -0.21 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  57 
 HIS   0.004   0.001   HIS B 181 
 PHE   0.011   0.001   PHE C  67 
 TYR   0.013   0.001   TYR D  32 
 ARG   0.005   0.001   ARG D  31 

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

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

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  888 Ramachandran restraints generated.
    444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   11 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue ILE   14 is missing expected H atoms. Skipping.
Residue LEU   15 is missing expected H atoms. Skipping.
Residue VAL   16 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  101 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   83 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue MET   82 is missing expected H atoms. Skipping.
Residue LYS   86 is missing expected H atoms. Skipping.
Residue LYS  111 is missing expected H atoms. Skipping.
Evaluate side-chains
  122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.529 
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: B   44 LEU cc_start: 0.8236 (mt) cc_final: 0.8005 (mt)
REVERT: B   81 HIS cc_start: 0.7057 (m90) cc_final: 0.6629 (m90)
REVERT: B   96 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.6336 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6910 (t80) cc_final: 0.6561 (t80)
REVERT: D  101 TRP cc_start: 0.7955 (m100) cc_final: 0.7657 (m100)
REVERT: D  106 GLN cc_start: 0.8151 (pp30) cc_final: 0.7583 (pp30)
REVERT: C  113 THR cc_start: 0.8414 (t) cc_final: 0.8196 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 118
  average time/residue: 0.3335
  time to fit residues: 47.1843
Evaluate side-chains
  119 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  105 THR
Chi-restraints excluded: chain C residue  116 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** B 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.149678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.127382 restraints weight = 20861.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.133232 restraints weight = 9117.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136794 restraints weight = 4899.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.5156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3503  Z= 0.214
  Angle     :  0.590  10.046   4753  Z= 0.312
  Chirality :  0.044   0.141    512
  Planarity :  0.004   0.035    630
  Dihedral  :  4.449  15.125    493
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.62 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.41), residues: 444
  helix: -1.94 (0.94), residues: 25
  sheet:  0.34 (0.38), residues: 209
  loop : -0.25 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  47 
 HIS   0.005   0.001   HIS B 217 
 PHE   0.012   0.002   PHE C  67 
 TYR   0.018   0.002   TYR B 143 
 ARG   0.005   0.001   ARG D  31 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3479.09 seconds
wall clock time: 59 minutes 54.97 seconds (3594.97 seconds total)