Starting phenix.real_space_refine
on Wed Sep 17 07:27:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rle_19340/09_2025/8rle_19340.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rle_19340/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rle_19340/09_2025/8rle_19340.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rle_19340/09_2025/8rle_19340.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rle_19340/09_2025/8rle_19340.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rle_19340/09_2025/8rle_19340.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
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): 0.00s

  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: 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: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 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: 1.52, per 1000 atoms: 0.23
  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: 0.62
  Conformation dependent library (CDL) restraints added in 242.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.21
  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: 1.42

  Time building geometry restraints manager: 0.81 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:             2.820
  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:             0.050
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.360
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.730
-------------------------------------------------------------------------------
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   3506  Z= 0.163
  Angle     :  0.557   5.355   4759  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 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:  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
 ARG   0.004   0.001   ARG D  35 
 TYR   0.008   0.001   TYR B 143 
 PHE   0.020   0.001   PHE B 165 
 TRP   0.012   0.002   TRP D  47 
 HIS   0.005   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3503)
  covalent geometry    : angle       0.55725 ( 4753)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       0.38479 (    6)
  hydrogen bonds       : bond        0.10365 (  150)
  hydrogen bonds       : angle       6.62804 (  390)

*********************** 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  : 0.157 
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: 0.1616
  time to fit residues: 23.6593
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  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4206 r_free = 0.4206 target = 0.159571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.137207 restraints weight = 20999.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.143429 restraints weight = 9098.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.147184 restraints weight = 4792.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.149402 restraints weight = 2862.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.150736 restraints weight = 1930.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3506  Z= 0.153
  Angle     :  0.560   4.879   4759  Z= 0.302
  Chirality :  0.043   0.143    512
  Planarity :  0.004   0.034    630
  Dihedral  :  4.254  13.790    493
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.86 %
    Favored  : 86.44 %
  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:  0.40 (0.39), residues: 444
  helix: -0.93 (0.98), residues: 28
  sheet:  0.67 (0.37), residues: 211
  loop :  0.15 (0.41), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  98 
 TYR   0.011   0.001   TYR D  91 
 PHE   0.013   0.002   PHE C  67 
 TRP   0.007   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3503)
  covalent geometry    : angle       0.55996 ( 4753)
  SS BOND              : bond        0.00404 (    3)
  SS BOND              : angle       0.55523 (    6)
  hydrogen bonds       : bond        0.03880 (  150)
  hydrogen bonds       : angle       6.18130 (  390)

*********************** 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
  126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.191 
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: 0.8213 (mt) cc_final: 0.7949 (mt)
REVERT: B  170 ASN cc_start: 0.8922 (m110) cc_final: 0.8695 (m110)
REVERT: B  182 TYR cc_start: 0.6910 (t80) cc_final: 0.6474 (t80)
REVERT: C  113 THR cc_start: 0.8305 (t) cc_final: 0.8032 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 120
  average time/residue: 0.1589
  time to fit residues: 22.7835
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  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue  106 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
** 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 = 0.4179 r_free = 0.4179 target = 0.157653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.135646 restraints weight = 20892.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.141718 restraints weight = 9040.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.145285 restraints weight = 4748.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.147410 restraints weight = 2854.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.148653 restraints weight = 1956.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3506  Z= 0.149
  Angle     :  0.542   4.768   4759  Z= 0.291
  Chirality :  0.043   0.131    512
  Planarity :  0.004   0.033    630
  Dihedral  :  4.224  14.036    493
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 16.38 %
    Favored  : 82.20 %
  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:  0.35 (0.40), residues: 444
  helix: -1.77 (0.94), residues: 25
  sheet:  0.66 (0.37), residues: 210
  loop :  0.18 (0.41), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  71 
 TYR   0.011   0.001   TYR D  91 
 PHE   0.020   0.002   PHE C  67 
 TRP   0.010   0.001   TRP D 101 
 HIS   0.004   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3503)
  covalent geometry    : angle       0.54176 ( 4753)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       0.87391 (    6)
  hydrogen bonds       : bond        0.03707 (  150)
  hydrogen bonds       : angle       6.10632 (  390)

*********************** 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
  125 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.199 
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: 0.8168 (mt) cc_final: 0.7912 (mt)
REVERT: B   96 ARG cc_start: 0.6436 (mtp180) cc_final: 0.6161 (mtp180)
REVERT: B  182 TYR cc_start: 0.6898 (t80) cc_final: 0.6469 (t80)
REVERT: B  204 GLN cc_start: 0.7856 (tt0) cc_final: 0.7607 (tt0)
REVERT: B  218 MET cc_start: 0.8561 (mpp) cc_final: 0.8253 (mpp)
REVERT: D   71 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6185 (ttp-170)
REVERT: D  106 GLN cc_start: 0.8066 (pp30) cc_final: 0.7832 (pp30)
REVERT: C  113 THR cc_start: 0.8302 (t) cc_final: 0.8102 (t)
  outliers start: 5
  outliers final: 3
  residues processed: 121
  average time/residue: 0.1808
  time to fit residues: 25.8096
Evaluate side-chains
  121 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 135 ASN
B 177 GLN
C   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.155868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.133557 restraints weight = 20619.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.139567 restraints weight = 8862.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.143155 restraints weight = 4644.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.145316 restraints weight = 2799.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.146469 restraints weight = 1923.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3506  Z= 0.141
  Angle     :  0.523   4.768   4759  Z= 0.281
  Chirality :  0.043   0.136    512
  Planarity :  0.004   0.033    630
  Dihedral  :  4.188  14.726    493
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 17.23 %
    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 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:  0.37 (0.41), residues: 444
  helix: -1.73 (0.95), residues: 25
  sheet:  0.52 (0.36), residues: 216
  loop :  0.37 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  35 
 TYR   0.012   0.001   TYR D  91 
 PHE   0.012   0.001   PHE C  67 
 TRP   0.004   0.001   TRP D 101 
 HIS   0.004   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3503)
  covalent geometry    : angle       0.52181 ( 4753)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       0.94998 (    6)
  hydrogen bonds       : bond        0.03534 (  150)
  hydrogen bonds       : angle       6.04222 (  390)

*********************** 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
  118 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 LEU cc_start: 0.8197 (mt) cc_final: 0.7924 (mt)
REVERT: B  182 TYR cc_start: 0.6959 (t80) cc_final: 0.6515 (t80)
REVERT: B  204 GLN cc_start: 0.7888 (tt0) cc_final: 0.7594 (tt0)
REVERT: D  106 GLN cc_start: 0.8058 (pp30) cc_final: 0.7741 (pp30)
REVERT: C   71 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7360 (ttm110)
REVERT: C  113 THR cc_start: 0.8345 (t) cc_final: 0.8128 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 115
  average time/residue: 0.1819
  time to fit residues: 24.6243
Evaluate side-chains
  114 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 24 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.154002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.131764 restraints weight = 20788.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.137830 restraints weight = 8908.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.141387 restraints weight = 4681.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.143572 restraints weight = 2823.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.144869 restraints weight = 1918.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3506  Z= 0.156
  Angle     :  0.548   4.961   4759  Z= 0.292
  Chirality :  0.043   0.129    512
  Planarity :  0.004   0.040    630
  Dihedral  :  4.288  14.405    493
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 19.49 %
    Favored  : 79.38 %
  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:  0.08 (0.40), residues: 444
  helix: -1.75 (0.97), residues: 25
  sheet:  0.30 (0.36), residues: 220
  loop :  0.20 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  35 
 TYR   0.014   0.001   TYR C  79 
 PHE   0.013   0.001   PHE C  67 
 TRP   0.005   0.001   TRP C 109 
 HIS   0.004   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3503)
  covalent geometry    : angle       0.54705 ( 4753)
  SS BOND              : bond        0.00119 (    3)
  SS BOND              : angle       1.20135 (    6)
  hydrogen bonds       : bond        0.03753 (  150)
  hydrogen bonds       : angle       6.09855 (  390)

*********************** 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
  126 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.177 
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: B   44 LEU cc_start: 0.8206 (mt) cc_final: 0.7938 (mt)
REVERT: B  182 TYR cc_start: 0.6854 (t80) cc_final: 0.6451 (t80)
REVERT: D  106 GLN cc_start: 0.8088 (pp30) cc_final: 0.7703 (pp30)
REVERT: C   19 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7331 (mtm180)
REVERT: C   98 ARG cc_start: 0.6918 (ttp80) cc_final: 0.6610 (ttp80)
  outliers start: 4
  outliers final: 2
  residues processed: 124
  average time/residue: 0.1829
  time to fit residues: 26.6754
Evaluate side-chains
  118 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   77 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:    0.0570
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0000
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4304

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

Flipped N/Q/H residues before XYZ refinement:
B 177 GLN
B 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.155263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.133564 restraints weight = 20943.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.139480 restraints weight = 8957.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.143042 restraints weight = 4699.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.145170 restraints weight = 2826.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.146368 restraints weight = 1928.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3506  Z= 0.106
  Angle     :  0.521   5.154   4759  Z= 0.273
  Chirality :  0.043   0.131    512
  Planarity :  0.003   0.035    630
  Dihedral  :  4.112  13.391    493
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 20.34 %
    Favored  : 78.25 %
  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:  0.33 (0.40), residues: 444
  helix: -1.65 (1.00), residues: 25
  sheet:  0.65 (0.37), residues: 206
  loop :  0.15 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  45 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.010   0.001   PHE C  67 
 TRP   0.007   0.001   TRP C 109 
 HIS   0.002   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 3503)
  covalent geometry    : angle       0.51915 ( 4753)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       1.20461 (    6)
  hydrogen bonds       : bond        0.03173 (  150)
  hydrogen bonds       : angle       5.93399 (  390)

*********************** 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: 5
    poor density    : 118
  time to evaluate  : 0.194 
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: 0.8227 (mt) cc_final: 0.7981 (mt)
REVERT: B   81 HIS cc_start: 0.6651 (m90) cc_final: 0.6324 (m90)
REVERT: B  182 TYR cc_start: 0.6817 (t80) cc_final: 0.6426 (t80)
REVERT: D   31 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7546 (mtt90)
REVERT: D  101 TRP cc_start: 0.7793 (m100) cc_final: 0.7221 (m100)
REVERT: D  106 GLN cc_start: 0.8047 (pp30) cc_final: 0.7608 (pp30)
REVERT: C   98 ARG cc_start: 0.6881 (ttp80) cc_final: 0.6545 (ttp80)
  outliers start: 5
  outliers final: 2
  residues processed: 121
  average time/residue: 0.1950
  time to fit residues: 27.5321
Evaluate side-chains
  118 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 8 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.148159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.126300 restraints weight = 20373.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.132085 restraints weight = 8873.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.135647 restraints weight = 4757.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.137800 restraints weight = 2935.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.139159 restraints weight = 2051.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3506  Z= 0.252
  Angle     :  0.636   5.998   4759  Z= 0.349
  Chirality :  0.044   0.129    512
  Planarity :  0.006   0.061    630
  Dihedral  :  4.992  16.227    493
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.49 %
    Favored  : 76.84 %
  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: -0.39 (0.40), residues: 444
  helix: -2.28 (0.90), residues: 25
  sheet:  0.17 (0.36), residues: 219
  loop : -0.33 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  35 
 TYR   0.019   0.002   TYR C  79 
 PHE   0.018   0.002   PHE C 102 
 TRP   0.009   0.002   TRP D  36 
 HIS   0.007   0.002   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 3503)
  covalent geometry    : angle       0.63427 ( 4753)
  SS BOND              : bond        0.00145 (    3)
  SS BOND              : angle       1.55199 (    6)
  hydrogen bonds       : bond        0.04682 (  150)
  hydrogen bonds       : angle       6.59736 (  390)

*********************** 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
  138 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.189 
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   43 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7593 (p)
REVERT: B   44 LEU cc_start: 0.8289 (mt) cc_final: 0.7985 (mt)
REVERT: B  182 TYR cc_start: 0.6767 (t80) cc_final: 0.6441 (t80)
REVERT: D   95 ASN cc_start: 0.8072 (p0) cc_final: 0.7775 (p0)
REVERT: C   98 ARG cc_start: 0.6863 (ttp80) cc_final: 0.6524 (ttp80)
  outliers start: 13
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1847
  time to fit residues: 28.2661
Evaluate side-chains
  131 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   86 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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
C   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.150625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.128996 restraints weight = 20850.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.134791 restraints weight = 9074.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.138380 restraints weight = 4884.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.140617 restraints weight = 3000.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.141927 restraints weight = 2057.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3506  Z= 0.132
  Angle     :  0.566   5.869   4759  Z= 0.302
  Chirality :  0.044   0.140    512
  Planarity :  0.004   0.035    630
  Dihedral  :  4.472  14.341    493
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.01 %
    Favored  : 74.86 %
  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: -0.25 (0.40), residues: 444
  helix: -2.11 (0.90), residues: 25
  sheet:  0.42 (0.37), residues: 199
  loop : -0.40 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  39 
 TYR   0.012   0.001   TYR D  32 
 PHE   0.016   0.002   PHE D  67 
 TRP   0.011   0.001   TRP D 101 
 HIS   0.007   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3503)
  covalent geometry    : angle       0.56414 ( 4753)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       1.52858 (    6)
  hydrogen bonds       : bond        0.03590 (  150)
  hydrogen bonds       : angle       6.29484 (  390)

*********************** 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: 4
    poor density    : 121
  time to evaluate  : 0.224 
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: 0.8234 (mt) cc_final: 0.8000 (mt)
REVERT: B   81 HIS cc_start: 0.6806 (m90) cc_final: 0.6486 (m90)
REVERT: B   96 ARG cc_start: 0.6423 (mtp180) cc_final: 0.6032 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6826 (t80) cc_final: 0.6508 (t80)
REVERT: D   95 ASN cc_start: 0.7703 (p0) cc_final: 0.7413 (p0)
REVERT: D  106 GLN cc_start: 0.8121 (pp30) cc_final: 0.7637 (pp30)
REVERT: C   98 ARG cc_start: 0.6813 (ttp80) cc_final: 0.6523 (ttp80)
REVERT: C  109 TRP cc_start: 0.8807 (m100) cc_final: 0.8453 (m100)
  outliers start: 4
  outliers final: 3
  residues processed: 124
  average time/residue: 0.1748
  time to fit residues: 25.6139
Evaluate side-chains
  123 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 GLN
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   89 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    0.4980
   chunk 1 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.148472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.126742 restraints weight = 20722.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.132515 restraints weight = 8986.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.136029 restraints weight = 4833.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.138225 restraints weight = 2993.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.139582 restraints weight = 2067.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3506  Z= 0.176
  Angle     :  0.594   6.827   4759  Z= 0.317
  Chirality :  0.044   0.131    512
  Planarity :  0.005   0.061    630
  Dihedral  :  4.620  14.357    493
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 23.73 %
    Favored  : 74.86 %
  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: -0.32 (0.40), residues: 444
  helix: -1.59 (0.94), residues: 28
  sheet:  0.39 (0.37), residues: 199
  loop : -0.53 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  35 
 TYR   0.016   0.002   TYR D  32 
 PHE   0.014   0.002   PHE D  67 
 TRP   0.008   0.002   TRP D 101 
 HIS   0.006   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3503)
  covalent geometry    : angle       0.59138 ( 4753)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       1.53866 (    6)
  hydrogen bonds       : bond        0.03982 (  150)
  hydrogen bonds       : angle       6.42503 (  390)

*********************** 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
  124 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 119
  time to evaluate  : 0.199 
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: 0.8259 (mt) cc_final: 0.8020 (mt)
REVERT: B   96 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6100 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6745 (t80) cc_final: 0.6475 (t80)
REVERT: D   95 ASN cc_start: 0.7868 (p0) cc_final: 0.7585 (p0)
REVERT: C   98 ARG cc_start: 0.6828 (ttp80) cc_final: 0.6546 (ttp80)
  outliers start: 5
  outliers final: 3
  residues processed: 121
  average time/residue: 0.1707
  time to fit residues: 24.5538
Evaluate side-chains
  122 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0370
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.149401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.127831 restraints weight = 20608.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.133569 restraints weight = 8916.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.137064 restraints weight = 4766.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.139219 restraints weight = 2941.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.140565 restraints weight = 2044.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.5294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3506  Z= 0.142
  Angle     :  0.593  11.612   4759  Z= 0.309
  Chirality :  0.044   0.137    512
  Planarity :  0.005   0.046    630
  Dihedral  :  4.478  13.601    493
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 24.01 %
    Favored  : 74.58 %
  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: -0.31 (0.41), residues: 444
  helix: -1.53 (0.96), residues: 28
  sheet:  0.39 (0.38), residues: 199
  loop : -0.52 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  35 
 TYR   0.015   0.001   TYR D  32 
 PHE   0.011   0.002   PHE C  67 
 TRP   0.010   0.001   TRP D 101 
 HIS   0.006   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3503)
  covalent geometry    : angle       0.59103 ( 4753)
  SS BOND              : bond        0.00190 (    3)
  SS BOND              : angle       1.54531 (    6)
  hydrogen bonds       : bond        0.03593 (  150)
  hydrogen bonds       : angle       6.32836 (  390)

********************** 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: 5
    poor density    : 117
  time to evaluate  : 0.191 
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: 0.8248 (mt) cc_final: 0.7959 (mt)
REVERT: B   81 HIS cc_start: 0.6823 (m90) cc_final: 0.6501 (m90)
REVERT: B   96 ARG cc_start: 0.6450 (mtp180) cc_final: 0.6069 (mtp-110)
REVERT: B  182 TYR cc_start: 0.6764 (t80) cc_final: 0.6489 (t80)
REVERT: B  204 GLN cc_start: 0.7730 (tt0) cc_final: 0.7491 (tt0)
REVERT: D   95 ASN cc_start: 0.7735 (p0) cc_final: 0.7429 (p0)
REVERT: D   98 PHE cc_start: 0.7800 (m-80) cc_final: 0.7531 (m-80)
REVERT: C   98 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6549 (ttp80)
  outliers start: 5
  outliers final: 3
  residues processed: 121
  average time/residue: 0.1599
  time to fit residues: 23.1129
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  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4081 r_free = 0.4081 target = 0.148930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.127257 restraints weight = 20672.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.133018 restraints weight = 9020.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.136517 restraints weight = 4846.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.138724 restraints weight = 3007.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.140083 restraints weight = 2080.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.5440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3506  Z= 0.146
  Angle     :  0.589   8.764   4759  Z= 0.310
  Chirality :  0.044   0.141    512
  Planarity :  0.005   0.037    630
  Dihedral  :  4.489  13.769    493
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 23.16 %
    Favored  : 75.14 %
  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: -0.36 (0.41), residues: 444
  helix: -1.92 (0.96), residues: 24
  sheet:  0.33 (0.37), residues: 205
  loop : -0.52 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  35 
 TYR   0.013   0.001   TYR D  32 
 PHE   0.011   0.002   PHE C  67 
 TRP   0.007   0.001   TRP B  57 
 HIS   0.005   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3503)
  covalent geometry    : angle       0.58752 ( 4753)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       1.45961 (    6)
  hydrogen bonds       : bond        0.03673 (  150)
  hydrogen bonds       : angle       6.29714 (  390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2028.62 seconds
wall clock time: 35 minutes 13.10 seconds (2113.10 seconds total)