Starting phenix.real_space_refine
on Fri Aug 22 19:49:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hlb_34871/08_2025/8hlb_34871.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.034
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: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4672      2.51       5
     N    1257      2.21       5
     O    1494      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7461
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 868
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 7, 'TRANS': 104}
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1622
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1662
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203}
    Chain: "D"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1675
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 12, 'TRANS': 208}
    Chain: "E"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1634
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201}
  Time building chain proxies: 2.02, per 1000 atoms: 0.27
  Number of scatterers: 7461
  At special positions: 0
  Unit cell: (65.25, 97.875, 130.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1494      8.00
     N    1257      7.00
     C    4672      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A  31 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A  45 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 138 " - pdb=" SG  CYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 146 " - pdb=" SG  CYS D 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 134 " - pdb=" SG  CYS E 194 " distance=2.04

  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: 0.75
  Conformation dependent library (CDL) restraints added in 449.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1816

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 25 sheets defined
      5.4% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 160 through 162
      No H-bonds generated for 'chain 'B' and resid 160 through 162'
    Processing helix  chain 'B' and resid 189 through 193
      removed outlier: 3.684A  pdb=" N   SER B 192 " --> pdb=" O   PRO B 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 132
    Processing helix  chain 'C' and resid 187 through 191
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.875A  pdb=" N   SER D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.587A  pdb=" N   GLY D 139 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 164
      No H-bonds generated for 'chain 'D' and resid 162 through 164'
    Processing helix  chain 'D' and resid 191 through 196
      removed outlier: 4.298A  pdb=" N   GLY D 196 " --> pdb=" O   SER D 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 128
    Processing helix  chain 'E' and resid 185 through 189
      removed outlier: 3.668A  pdb=" N   HIS E 189 " --> pdb=" O   TYR E 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43
      removed outlier: 7.219A  pdb=" N   VAL A  52 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 58
      removed outlier: 5.080A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   MET B  50 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   VAL B  34 " --> pdb=" O   MET B  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 128
      removed outlier: 6.101A  pdb=" N   TYR B 180 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B 181 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 158
      removed outlier: 4.320A  pdb=" N   TYR B 198 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7
      removed outlier: 4.056A  pdb=" N   CYS C  23 " --> pdb=" O   PHE C  75 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   PHE C  75 " --> pdb=" O   CYS C  23 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR C  76 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.790A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 38
    Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 42
    Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 122
      removed outlier: 3.584A  pdb=" N   SER C 181 " --> pdb=" O   CYS C 138 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158
      removed outlier: 3.678A  pdb=" N   GLN C 151 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 5
    Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.580A  pdb=" N   LEU D 115 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   TRP D  36 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.580A  pdb=" N   LEU D 115 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 126 through 129
      removed outlier: 3.822A  pdb=" N   PHE D 128 " --> pdb=" O   LEU D 147 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER D 186 " --> pdb=" O   CYS D 146 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 158 through 160
    Processing sheet with id=AC2, first strand: chain 'D' and resid 175 through 176
      removed outlier: 3.539A  pdb=" N   SER D 183 " --> pdb=" O   VAL D 175 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 12 through 13
    Processing sheet with id=AC4, first strand: chain 'E' and resid 22 through 24
      removed outlier: 3.712A  pdb=" N   ASP E  70 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER E  67 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 54
      removed outlier: 6.311A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR E  86 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR E 102 " --> pdb=" O   TYR E  86 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 117
    Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 150

    177 hydrogen bonds defined for protein.
    411 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: 1.09

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2354
        1.34 -     1.46: 1570
        1.46 -     1.58: 3668
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 7636
  Sorted by residual:
  bond pdb=" N   GLN A  82 "
       pdb=" CA  GLN A  82 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 1.19e-02 7.06e+03 5.65e+00
  bond pdb=" N   ASP A  81 "
       pdb=" CA  ASP A  81 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.52e-02 4.33e+03 4.36e+00
  bond pdb=" C   TYR E  36 "
       pdb=" N   GLN E  37 "
    ideal  model  delta    sigma   weight residual
    1.330  1.303  0.027 1.39e-02 5.18e+03 3.74e+00
  bond pdb=" N   TYR E  36 "
       pdb=" CA  TYR E  36 "
    ideal  model  delta    sigma   weight residual
    1.455  1.476 -0.021 1.23e-02 6.61e+03 2.89e+00
  bond pdb=" C   GLU D 154 "
       pdb=" N   PRO D 155 "
    ideal  model  delta    sigma   weight residual
    1.332  1.350 -0.018 1.12e-02 7.97e+03 2.44e+00
  ... (remaining 7631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 10052
        1.61 -     3.21: 285
        3.21 -     4.82: 44
        4.82 -     6.42: 7
        6.42 -     8.03: 4
  Bond angle restraints: 10392
  Sorted by residual:
  angle pdb=" C   SER A  79 "
        pdb=" CA  SER A  79 "
        pdb=" CB  SER A  79 "
      ideal   model   delta    sigma   weight residual
     116.63  110.25    6.38 1.16e+00 7.43e-01 3.03e+01
  angle pdb=" CA  SER A  79 "
        pdb=" C   SER A  79 "
        pdb=" N   SER A  80 "
      ideal   model   delta    sigma   weight residual
     119.63  116.78    2.85 8.10e-01 1.52e+00 1.24e+01
  angle pdb=" CA  GLN E  89 "
        pdb=" C   GLN E  89 "
        pdb=" O   GLN E  89 "
      ideal   model   delta    sigma   weight residual
     121.06  117.19    3.87 1.16e+00 7.43e-01 1.11e+01
  angle pdb=" C   GLN E  89 "
        pdb=" CA  GLN E  89 "
        pdb=" CB  GLN E  89 "
      ideal   model   delta    sigma   weight residual
     109.56  102.50    7.06 2.22e+00 2.03e-01 1.01e+01
  angle pdb=" O   TYR D 103 "
        pdb=" C   TYR D 103 "
        pdb=" N   VAL D 104 "
      ideal   model   delta    sigma   weight residual
     122.25  125.97   -3.72 1.18e+00 7.18e-01 9.93e+00
  ... (remaining 10387 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 4110
       16.01 -    32.02: 353
       32.02 -    48.04: 113
       48.04 -    64.05: 17
       64.05 -    80.06: 10
  Dihedral angle restraints: 4603
    sinusoidal: 1769
      harmonic: 2834
  Sorted by residual:
  dihedral pdb=" CB  CYS A  98 "
           pdb=" SG  CYS A  98 "
           pdb=" SG  CYS A 115 "
           pdb=" CB  CYS A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.36  -69.36     1      1.00e+01 1.00e-02 6.22e+01
  dihedral pdb=" CB  CYS A 104 "
           pdb=" SG  CYS A 104 "
           pdb=" SG  CYS A 112 "
           pdb=" CB  CYS A 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.10  -68.10     1      1.00e+01 1.00e-02 6.02e+01
  dihedral pdb=" CB  CYS A  18 "
           pdb=" SG  CYS A  18 "
           pdb=" SG  CYS A  31 "
           pdb=" CB  CYS A  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.13  -67.13     1      1.00e+01 1.00e-02 5.87e+01
  ... (remaining 4600 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 894
       0.043 -    0.087: 187
       0.087 -    0.130: 83
       0.130 -    0.173: 6
       0.173 -    0.216: 2
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  GLN E  89 "
            pdb=" N   GLN E  89 "
            pdb=" C   GLN E  89 "
            pdb=" CB  GLN E  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  ILE D  48 "
            pdb=" N   ILE D  48 "
            pdb=" C   ILE D  48 "
            pdb=" CB  ILE D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 1169 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  43 "    0.066 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO E  44 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO E  44 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO E  44 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  80 "   -0.034 5.00e-02 4.00e+02   5.11e-02 4.17e+00
        pdb=" N   PRO C  81 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C  81 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  81 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E  38 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.37e+00
        pdb=" C   GLN E  38 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLN E  38 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS E  39 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 666
        2.74 -     3.28: 7361
        3.28 -     3.82: 11738
        3.82 -     4.36: 13697
        4.36 -     4.90: 23984
  Nonbonded interactions: 57446
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 110 "
            pdb=" OH  TYR C 144 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   ASP A  81 "
            pdb=" OH  TYR D 103 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   SER E  30 "
            pdb=" OH  TYR E  71 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   VAL C  29 "
            pdb=" ND2 ASN C  96 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG  SER E 121 "
            pdb=" OE1 GLU E 123 "
     model   vdw
     2.277 3.040
  ... (remaining 57441 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.820
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
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   0.034   7652  Z= 0.147
  Angle     :  0.655   8.026  10424  Z= 0.353
  Chirality :  0.044   0.216   1172
  Planarity :  0.005   0.100   1327
  Dihedral  : 13.637  80.061   2739
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.38 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.13 (0.27), residues: 967
  helix: -0.35 (1.20), residues: 22
  sheet: -0.98 (0.28), residues: 362
  loop : -1.78 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  24 
 TYR   0.021   0.002   TYR E 140 
 PHE   0.021   0.002   PHE E 139 
 TRP   0.013   0.001   TRP B  52 
 HIS   0.003   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7636)
  covalent geometry    : angle       0.65397 (10392)
  SS BOND              : bond        0.00316 (   16)
  SS BOND              : angle       0.82350 (   32)
  hydrogen bonds       : bond        0.19616 (  173)
  hydrogen bonds       : angle       8.04598 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B   86 GLN cc_start: 0.7289 (mm-40) cc_final: 0.7054 (mp10)
REVERT: C    2 ILE cc_start: 0.8155 (mm) cc_final: 0.7928 (mm)
REVERT: C   52 ILE cc_start: 0.9261 (mm) cc_final: 0.9059 (mm)
REVERT: C  135 SER cc_start: 0.7864 (p) cc_final: 0.7602 (p)
REVERT: C  149 LYS cc_start: 0.8001 (tttm) cc_final: 0.7631 (tttm)
REVERT: C  174 ASP cc_start: 0.8622 (p0) cc_final: 0.8245 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0916
  time to fit residues: 17.2047
Evaluate side-chains
  119 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  82 GLN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.170174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140338 restraints weight = 9739.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140015 restraints weight = 7095.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142018 restraints weight = 6870.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.142234 restraints weight = 4889.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.142905 restraints weight = 5018.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7652  Z= 0.198
  Angle     :  0.656   7.334  10424  Z= 0.345
  Chirality :  0.046   0.190   1172
  Planarity :  0.005   0.067   1327
  Dihedral  :  4.833  22.551   1048
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  9.20 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.52 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.21 (0.27), residues: 967
  helix: -0.07 (1.20), residues: 22
  sheet: -1.02 (0.28), residues: 357
  loop : -1.86 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  18 
 TYR   0.030   0.002   TYR B 102 
 PHE   0.020   0.002   PHE B  79 
 TRP   0.015   0.002   TRP B 107 
 HIS   0.007   0.002   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7636)
  covalent geometry    : angle       0.65423 (10392)
  SS BOND              : bond        0.00478 (   16)
  SS BOND              : angle       1.12328 (   32)
  hydrogen bonds       : bond        0.03470 (  173)
  hydrogen bonds       : angle       6.79573 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 GLN cc_start: 0.7359 (mm-40) cc_final: 0.6995 (mp10)
REVERT: C    2 ILE cc_start: 0.8375 (mm) cc_final: 0.8138 (mm)
REVERT: C   52 ILE cc_start: 0.9364 (mm) cc_final: 0.9128 (mm)
REVERT: C  135 SER cc_start: 0.8105 (p) cc_final: 0.7872 (p)
REVERT: C  149 LYS cc_start: 0.7909 (tttm) cc_final: 0.7515 (tttm)
REVERT: C  174 ASP cc_start: 0.8471 (p0) cc_final: 0.8006 (p0)
REVERT: C  176 THR cc_start: 0.7384 (m) cc_final: 0.6722 (m)
REVERT: E   98 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7041 (m-10)
REVERT: E  195 GLU cc_start: 0.7659 (pp20) cc_final: 0.7211 (pp20)
  outliers start: 9
  outliers final: 6
  residues processed: 138
  average time/residue: 0.0892
  time to fit residues: 16.8737
Evaluate side-chains
  126 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  135 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 73 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B 208 ASN
C 151 GLN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.140888 restraints weight = 9859.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.139612 restraints weight = 7419.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.141179 restraints weight = 8157.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141879 restraints weight = 5521.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.143131 restraints weight = 5159.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7652  Z= 0.155
  Angle     :  0.624   6.989  10424  Z= 0.326
  Chirality :  0.044   0.161   1172
  Planarity :  0.005   0.052   1327
  Dihedral  :  4.827  22.395   1048
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.48 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.34 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.21 (0.27), residues: 967
  helix: -0.17 (1.14), residues: 22
  sheet: -1.02 (0.28), residues: 359
  loop : -1.86 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.029   0.002   TYR B 102 
 PHE   0.018   0.002   PHE B  79 
 TRP   0.013   0.001   TRP A  67 
 HIS   0.005   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7636)
  covalent geometry    : angle       0.62264 (10392)
  SS BOND              : bond        0.00354 (   16)
  SS BOND              : angle       1.03837 (   32)
  hydrogen bonds       : bond        0.03086 (  173)
  hydrogen bonds       : angle       6.63228 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5565 (mmm160)
REVERT: C    2 ILE cc_start: 0.8419 (mm) cc_final: 0.8175 (mm)
REVERT: C   52 ILE cc_start: 0.9347 (mm) cc_final: 0.9101 (mm)
REVERT: C  174 ASP cc_start: 0.8547 (p0) cc_final: 0.8158 (p0)
REVERT: E   92 TYR cc_start: 0.7079 (m-80) cc_final: 0.6748 (m-80)
REVERT: E  195 GLU cc_start: 0.7775 (pp20) cc_final: 0.7287 (pp20)
  outliers start: 18
  outliers final: 12
  residues processed: 137
  average time/residue: 0.0886
  time to fit residues: 16.7728
Evaluate side-chains
  134 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  208 ASN
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  185 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0000
   chunk 33 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 208 ASN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.168825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.138451 restraints weight = 10088.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.137555 restraints weight = 7373.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139126 restraints weight = 7224.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139568 restraints weight = 5413.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140177 restraints weight = 5539.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7652  Z= 0.193
  Angle     :  0.664   9.712  10424  Z= 0.346
  Chirality :  0.045   0.155   1172
  Planarity :  0.005   0.046   1327
  Dihedral  :  4.960  23.514   1048
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  9.62 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.28 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.21 (0.27), residues: 967
  helix: -0.12 (1.14), residues: 22
  sheet: -0.86 (0.29), residues: 342
  loop : -1.97 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  66 
 TYR   0.036   0.002   TYR B 102 
 PHE   0.025   0.002   PHE B  79 
 TRP   0.015   0.002   TRP A  67 
 HIS   0.007   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7636)
  covalent geometry    : angle       0.66187 (10392)
  SS BOND              : bond        0.00406 (   16)
  SS BOND              : angle       1.09298 (   32)
  hydrogen bonds       : bond        0.03202 (  173)
  hydrogen bonds       : angle       6.69480 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: B  101 ARG cc_start: 0.6063 (mmm160) cc_final: 0.5640 (mmm160)
REVERT: C   52 ILE cc_start: 0.9367 (mm) cc_final: 0.9128 (mm)
REVERT: C  174 ASP cc_start: 0.8408 (p0) cc_final: 0.7936 (p0)
REVERT: C  192 LYS cc_start: 0.7560 (tptp) cc_final: 0.7335 (tptp)
REVERT: E   92 TYR cc_start: 0.7340 (m-80) cc_final: 0.6757 (m-80)
REVERT: E   98 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7059 (m-10)
REVERT: E  195 GLU cc_start: 0.7817 (pp20) cc_final: 0.7307 (pp20)
  outliers start: 19
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0834
  time to fit residues: 16.7644
Evaluate side-chains
  139 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  151 ASP
Chi-restraints excluded: chain E residue  152 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
B  86 GLN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
E  38 GLN
E  91 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.169375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.138949 restraints weight = 10027.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.137570 restraints weight = 7532.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139334 restraints weight = 8258.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.139891 restraints weight = 5600.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141097 restraints weight = 5289.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7652  Z= 0.173
  Angle     :  0.657   9.299  10424  Z= 0.341
  Chirality :  0.045   0.152   1172
  Planarity :  0.005   0.043   1327
  Dihedral  :  4.947  23.199   1048
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.58 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.92 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.21 (0.27), residues: 967
  helix: -0.07 (1.11), residues: 22
  sheet: -0.85 (0.29), residues: 330
  loop : -1.97 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.034   0.002   TYR B 102 
 PHE   0.023   0.002   PHE B  79 
 TRP   0.015   0.002   TRP A  67 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7636)
  covalent geometry    : angle       0.65527 (10392)
  SS BOND              : bond        0.00366 (   16)
  SS BOND              : angle       1.06197 (   32)
  hydrogen bonds       : bond        0.03085 (  173)
  hydrogen bonds       : angle       6.60350 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7798 (mtp180)
REVERT: B  101 ARG cc_start: 0.6114 (mmm160) cc_final: 0.4924 (mmm160)
REVERT: C   52 ILE cc_start: 0.9356 (mm) cc_final: 0.9113 (mm)
REVERT: C   57 ASN cc_start: 0.8068 (m-40) cc_final: 0.7791 (m110)
REVERT: C  174 ASP cc_start: 0.8407 (p0) cc_final: 0.7959 (p0)
REVERT: C  192 LYS cc_start: 0.7611 (tptp) cc_final: 0.7379 (tptp)
REVERT: E   38 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8226 (tm-30)
REVERT: E   98 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6954 (m-10)
REVERT: E  118 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7437 (p90)
REVERT: E  195 GLU cc_start: 0.7808 (pp20) cc_final: 0.7309 (pp20)
  outliers start: 24
  outliers final: 14
  residues processed: 144
  average time/residue: 0.0902
  time to fit residues: 17.8019
Evaluate side-chains
  137 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  162 ASN
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   38 GLN
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  151 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 74 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 208 ASN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.170290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.139911 restraints weight = 10020.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.138629 restraints weight = 7372.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140213 restraints weight = 8355.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.140893 restraints weight = 5634.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.142160 restraints weight = 5285.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7652  Z= 0.146
  Angle     :  0.654   8.964  10424  Z= 0.334
  Chirality :  0.044   0.142   1172
  Planarity :  0.005   0.042   1327
  Dihedral  :  4.894  21.863   1048
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.27 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.33 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.20 (0.27), residues: 967
  helix:  0.00 (1.10), residues: 22
  sheet: -0.95 (0.29), residues: 340
  loop : -1.89 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.029   0.002   TYR B 102 
 PHE   0.022   0.002   PHE B  79 
 TRP   0.013   0.001   TRP A  67 
 HIS   0.005   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7636)
  covalent geometry    : angle       0.65267 (10392)
  SS BOND              : bond        0.00304 (   16)
  SS BOND              : angle       0.94857 (   32)
  hydrogen bonds       : bond        0.02925 (  173)
  hydrogen bonds       : angle       6.49436 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   30 MET cc_start: 0.6998 (ttm) cc_final: 0.6588 (ttp)
REVERT: B  101 ARG cc_start: 0.6078 (mmm160) cc_final: 0.4895 (mmm160)
REVERT: C   52 ILE cc_start: 0.9342 (mm) cc_final: 0.9102 (mm)
REVERT: C   57 ASN cc_start: 0.8040 (m-40) cc_final: 0.7777 (m110)
REVERT: C  174 ASP cc_start: 0.8530 (p0) cc_final: 0.8048 (p0)
REVERT: C  192 LYS cc_start: 0.7582 (tptp) cc_final: 0.7305 (tptp)
REVERT: D  144 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7956 (pp)
REVERT: E   98 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6846 (m-10)
REVERT: E  118 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7301 (p90)
REVERT: E  195 GLU cc_start: 0.7806 (pp20) cc_final: 0.7308 (pp20)
  outliers start: 26
  outliers final: 15
  residues processed: 147
  average time/residue: 0.0842
  time to fit residues: 17.1487
Evaluate side-chains
  136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  162 ASN
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  147 GLN
Chi-restraints excluded: chain E residue  151 ASP
Chi-restraints excluded: chain E residue  152 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  86 GLN
B 208 ASN
C 162 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.169688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139307 restraints weight = 9837.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139199 restraints weight = 7886.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.141163 restraints weight = 7795.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.141568 restraints weight = 5341.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142638 restraints weight = 5164.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7652  Z= 0.160
  Angle     :  0.662   9.406  10424  Z= 0.338
  Chirality :  0.045   0.204   1172
  Planarity :  0.005   0.042   1327
  Dihedral  :  4.937  21.710   1048
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.48 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.27 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.18 (0.27), residues: 967
  helix:  0.05 (1.10), residues: 22
  sheet: -0.85 (0.29), residues: 325
  loop : -1.93 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  99 
 TYR   0.030   0.002   TYR B 102 
 PHE   0.022   0.002   PHE B  79 
 TRP   0.013   0.002   TRP A  67 
 HIS   0.006   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7636)
  covalent geometry    : angle       0.66142 (10392)
  SS BOND              : bond        0.00404 (   16)
  SS BOND              : angle       0.91620 (   32)
  hydrogen bonds       : bond        0.02923 (  173)
  hydrogen bonds       : angle       6.43229 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   30 MET cc_start: 0.7035 (ttm) cc_final: 0.6636 (ttp)
REVERT: B  101 ARG cc_start: 0.6118 (mmm160) cc_final: 0.4907 (mmm160)
REVERT: C   52 ILE cc_start: 0.9342 (mm) cc_final: 0.9100 (mm)
REVERT: C   57 ASN cc_start: 0.8106 (m-40) cc_final: 0.7873 (m110)
REVERT: C  156 ASN cc_start: 0.7020 (m110) cc_final: 0.6796 (m-40)
REVERT: C  174 ASP cc_start: 0.8422 (p0) cc_final: 0.7962 (p0)
REVERT: C  192 LYS cc_start: 0.7694 (tptp) cc_final: 0.7404 (tptp)
REVERT: D  144 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7953 (pp)
REVERT: E   98 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.6812 (m-10)
REVERT: E  118 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7169 (p90)
REVERT: E  195 GLU cc_start: 0.7752 (pp20) cc_final: 0.7312 (pp20)
  outliers start: 22
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0901
  time to fit residues: 16.9052
Evaluate side-chains
  137 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue  208 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  162 ASN
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  151 ASP
Chi-restraints excluded: chain E residue  152 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0670
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 56 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  38 GLN
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.172699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.142630 restraints weight = 9705.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142659 restraints weight = 7874.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.144578 restraints weight = 7734.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.145068 restraints weight = 5276.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146139 restraints weight = 5036.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7652  Z= 0.122
  Angle     :  0.643  10.067  10424  Z= 0.325
  Chirality :  0.044   0.190   1172
  Planarity :  0.005   0.040   1327
  Dihedral  :  4.857  21.099   1048
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  7.86 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.86 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.13 (0.27), residues: 967
  helix:  0.11 (1.12), residues: 22
  sheet: -0.91 (0.28), residues: 340
  loop : -1.84 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  21 
 TYR   0.024   0.002   TYR B 102 
 PHE   0.022   0.002   PHE B  79 
 TRP   0.011   0.001   TRP A  67 
 HIS   0.004   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7636)
  covalent geometry    : angle       0.64173 (10392)
  SS BOND              : bond        0.00321 (   16)
  SS BOND              : angle       0.87187 (   32)
  hydrogen bonds       : bond        0.02681 (  173)
  hydrogen bonds       : angle       6.31850 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.7013 (ttm) cc_final: 0.6691 (ttp)
REVERT: A   77 ARG cc_start: 0.6778 (tpp-160) cc_final: 0.6118 (mmm160)
REVERT: C   52 ILE cc_start: 0.9388 (mm) cc_final: 0.9151 (mm)
REVERT: C   57 ASN cc_start: 0.8024 (m-40) cc_final: 0.7807 (m110)
REVERT: C  174 ASP cc_start: 0.8560 (p0) cc_final: 0.8078 (p0)
REVERT: C  192 LYS cc_start: 0.7709 (tptp) cc_final: 0.7414 (tptp)
REVERT: D  144 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8012 (pp)
REVERT: E  118 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7140 (p90)
REVERT: E  195 GLU cc_start: 0.7671 (pp20) cc_final: 0.7294 (pp20)
  outliers start: 22
  outliers final: 17
  residues processed: 142
  average time/residue: 0.0820
  time to fit residues: 16.2230
Evaluate side-chains
  139 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  151 ASP
Chi-restraints excluded: chain E residue  152 ASN
Chi-restraints excluded: chain E residue  164 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 91 optimal weight:    0.4980
   chunk 80 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0070
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
B  86 GLN
B 208 ASN
C  93 GLN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.173654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.143549 restraints weight = 9682.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143533 restraints weight = 7891.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.145464 restraints weight = 7816.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.145994 restraints weight = 5297.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.147126 restraints weight = 5046.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7652  Z= 0.120
  Angle     :  0.642  10.386  10424  Z= 0.324
  Chirality :  0.044   0.170   1172
  Planarity :  0.005   0.040   1327
  Dihedral  :  4.775  20.302   1048
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.76 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.92 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.04 (0.27), residues: 967
  helix:  0.23 (1.13), residues: 22
  sheet: -0.84 (0.28), residues: 340
  loop : -1.79 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  21 
 TYR   0.023   0.002   TYR B 102 
 PHE   0.023   0.002   PHE B  79 
 TRP   0.011   0.001   TRP A  67 
 HIS   0.003   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7636)
  covalent geometry    : angle       0.64160 (10392)
  SS BOND              : bond        0.00307 (   16)
  SS BOND              : angle       0.84558 (   32)
  hydrogen bonds       : bond        0.02563 (  173)
  hydrogen bonds       : angle       6.19113 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.6997 (ttm) cc_final: 0.6648 (ttp)
REVERT: C   52 ILE cc_start: 0.9371 (mm) cc_final: 0.9129 (mm)
REVERT: C  174 ASP cc_start: 0.8564 (p0) cc_final: 0.8083 (p0)
REVERT: C  192 LYS cc_start: 0.7699 (tptp) cc_final: 0.7393 (tptp)
REVERT: D  144 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (pp)
REVERT: E  118 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7112 (p90)
REVERT: E  195 GLU cc_start: 0.7677 (pp20) cc_final: 0.7290 (pp20)
  outliers start: 20
  outliers final: 15
  residues processed: 137
  average time/residue: 0.0833
  time to fit residues: 16.0889
Evaluate side-chains
  138 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue  208 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  164 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    0.1980
   chunk 57 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  86 GLN
C  57 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.175983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.146751 restraints weight = 9867.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.145627 restraints weight = 8213.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147201 restraints weight = 9356.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.148255 restraints weight = 5723.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.148803 restraints weight = 5155.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7652  Z= 0.124
  Angle     :  0.650  10.748  10424  Z= 0.328
  Chirality :  0.044   0.197   1172
  Planarity :  0.005   0.039   1327
  Dihedral  :  4.758  20.042   1048
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.76 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.39 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    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: -2.01 (0.27), residues: 967
  helix:  0.31 (1.16), residues: 22
  sheet: -0.86 (0.28), residues: 346
  loop : -1.74 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.022   0.002   TYR B 102 
 PHE   0.023   0.002   PHE B  79 
 TRP   0.014   0.001   TRP B  52 
 HIS   0.004   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7636)
  covalent geometry    : angle       0.64938 (10392)
  SS BOND              : bond        0.00328 (   16)
  SS BOND              : angle       0.89949 (   32)
  hydrogen bonds       : bond        0.02627 (  173)
  hydrogen bonds       : angle       6.16251 (  411)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.7038 (ttm) cc_final: 0.6400 (ttm)
REVERT: C   52 ILE cc_start: 0.9376 (mm) cc_final: 0.9126 (mm)
REVERT: C  176 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6943 (m)
REVERT: D  144 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8088 (pp)
REVERT: E  118 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7044 (p90)
REVERT: E  195 GLU cc_start: 0.7699 (pp20) cc_final: 0.7299 (pp20)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.0845
  time to fit residues: 15.9410
Evaluate side-chains
  136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  176 THR
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  118 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  164 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 63 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 208 ASN
C  57 ASN
** D  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 147 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.174015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.143912 restraints weight = 9577.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143797 restraints weight = 7888.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.145795 restraints weight = 7798.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.146334 restraints weight = 5252.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.147429 restraints weight = 4965.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7652  Z= 0.115
  Angle     :  0.630  10.610  10424  Z= 0.317
  Chirality :  0.043   0.165   1172
  Planarity :  0.005   0.039   1327
  Dihedral  :  4.659  19.578   1048
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.34 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.92 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.27), residues: 967
  helix:  0.35 (1.16), residues: 22
  sheet: -0.82 (0.28), residues: 346
  loop : -1.69 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.022   0.002   TYR B 102 
 PHE   0.024   0.002   PHE B  79 
 TRP   0.014   0.001   TRP B  52 
 HIS   0.003   0.001   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7636)
  covalent geometry    : angle       0.62983 (10392)
  SS BOND              : bond        0.00283 (   16)
  SS BOND              : angle       0.77350 (   32)
  hydrogen bonds       : bond        0.02561 (  173)
  hydrogen bonds       : angle       6.05459 (  411)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1320.13 seconds
wall clock time: 23 minutes 48.67 seconds (1428.67 seconds total)