Starting phenix.real_space_refine
on Fri Aug 22 15:04:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2c_42905/08_2025/8v2c_42905.map"
  }
  resolution = 3.46
  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=   0.016
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      23      5.16       5
     C    2886      2.51       5
     N     767      2.21       5
     O     924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s

  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: 4600
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1343
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 8, 'TRANS': 160}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1583
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 13, 'TRANS': 184}
    Chain: "C"
      Number of atoms: 1492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1492
          Classifications: {'peptide': 184}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.09, per 1000 atoms: 0.24
  Number of scatterers: 4600
  At special positions: 0
  Unit cell: (87.72, 102.34, 105.78, 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      23     16.00
     O     924      8.00
     N     767      7.00
     C    2886      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  71 " - pdb=" SG  CYS A 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 242 " - pdb=" SG  CYS C 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 275 " - pdb=" SG  CYS C 282 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG B 701 " - " ASN B 225 "
      " NAG B 702 " - " ASN B 157 "
      " NAG C 801 " - " ASN C 239 "
      " NAG D   1 " - " ASN B 131 "
      " NAG E   1 " - " ASN C 162 "
      " NAG F   1 " - " ASN C 271 "
      " NAG G   1 " - " ASN C 304 "
      " NAG H   1 " - " ASN C 323 "
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 118.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1048

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      26.5% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 47
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 80 through 87
    Processing helix  chain 'A' and resid 88 through 115
      removed outlier: 3.517A  pdb=" N   LEU A 115 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 144
      removed outlier: 4.475A  pdb=" N   ASP A 124 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 201
    Processing helix  chain 'B' and resid 213 through 216
    Processing helix  chain 'B' and resid 245 through 250
      removed outlier: 3.705A  pdb=" N   GLY B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 276
      removed outlier: 3.809A  pdb=" N   MET B 276 " --> pdb=" O   GLU B 273 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 181
      removed outlier: 3.631A  pdb=" N   CYS B 180 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 180 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN B 131 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   LYS B 219 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 219 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 173
    Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 173
    Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229
      removed outlier: 5.746A  pdb=" N   ASN B 225 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   VAL B 243 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 282 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269
    Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 151
    Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158
      removed outlier: 3.933A  pdb=" N   LYS C 155 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR C 226 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER C 177 " --> pdb=" O   GLN C 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241
      removed outlier: 6.707A  pdb=" N   ASN C 239 " --> pdb=" O   GLU C 255 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   GLU C 255 " --> pdb=" O   ASN C 239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274
      removed outlier: 3.886A  pdb=" N   TYR C 303 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   PHE C 322 " --> pdb=" O   TYR C 303 " (cutoff:3.500A)

    190 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.46

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1469
        1.34 -     1.46: 1142
        1.46 -     1.58: 2058
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 4700
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.57e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.15e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.00e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.87e+00
  ... (remaining 4695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 6148
        1.26 -     2.53: 186
        2.53 -     3.79: 40
        3.79 -     5.06: 2
        5.06 -     6.32: 3
  Bond angle restraints: 6379
  Sorted by residual:
  angle pdb=" N   GLY B 177 "
        pdb=" CA  GLY B 177 "
        pdb=" C   GLY B 177 "
      ideal   model   delta    sigma   weight residual
     110.95  114.28   -3.33 1.70e+00 3.46e-01 3.84e+00
  angle pdb=" CA  GLU A  54 "
        pdb=" C   GLU A  54 "
        pdb=" N   PRO A  55 "
      ideal   model   delta    sigma   weight residual
     118.44  121.50   -3.06 1.59e+00 3.96e-01 3.71e+00
  angle pdb=" CA  LYS A  89 "
        pdb=" C   LYS A  89 "
        pdb=" N   PRO A  90 "
      ideal   model   delta    sigma   weight residual
     118.44  121.28   -2.84 1.59e+00 3.96e-01 3.20e+00
  angle pdb=" N   THR A 117 "
        pdb=" CA  THR A 117 "
        pdb=" C   THR A 117 "
      ideal   model   delta    sigma   weight residual
     109.81  113.57   -3.76 2.21e+00 2.05e-01 2.89e+00
  angle pdb=" N   GLU A  54 "
        pdb=" CA  GLU A  54 "
        pdb=" C   GLU A  54 "
      ideal   model   delta    sigma   weight residual
     109.81  113.41   -3.60 2.21e+00 2.05e-01 2.66e+00
  ... (remaining 6374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.72: 2735
       21.72 -    43.44: 146
       43.44 -    65.15: 63
       65.15 -    86.87: 12
       86.87 -   108.59: 56
  Dihedral angle restraints: 3012
    sinusoidal: 1397
      harmonic: 1615
  Sorted by residual:
  dihedral pdb=" CB  CYS B 172 "
           pdb=" SG  CYS B 172 "
           pdb=" SG  CYS B 180 "
           pdb=" CB  CYS B 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.13  -51.13     1      1.00e+01 1.00e-02 3.58e+01
  dihedral pdb=" CB  CYS C 275 "
           pdb=" SG  CYS C 275 "
           pdb=" SG  CYS C 282 "
           pdb=" CB  CYS C 282 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.75  -45.25     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" C1  NAG E   1 "
           pdb=" C2  NAG E   1 "
           pdb=" C3  NAG E   1 "
           pdb=" O3  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.50 -108.59     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 3009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 664
       0.072 -    0.143: 81
       0.143 -    0.214: 0
       0.214 -    0.286: 0
       0.286 -    0.357: 1
  Chirality restraints: 746
  Sorted by residual:
  chirality pdb=" C1  NAG C 801 "
            pdb=" ND2 ASN C 239 "
            pdb=" C2  NAG C 801 "
            pdb=" O5  NAG C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  ILE A 150 "
            pdb=" N   ILE A 150 "
            pdb=" C   ILE A 150 "
            pdb=" CB  ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B 225 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 743 not shown)

  Planarity restraints: 810
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  64 "   -0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO A  65 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 213 "    0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO B 214 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 214 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 214 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 183 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO C 184 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 807 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1525
        2.85 -     3.36: 3796
        3.36 -     3.87: 6931
        3.87 -     4.39: 7285
        4.39 -     4.90: 13310
  Nonbonded interactions: 32847
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  38 "
            pdb=" OD2 ASP B 213 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG1 THR C 306 "
            pdb=" O6  NAG G   1 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" OE1 GLN C 270 "
            pdb=" NH2 ARG C 288 "
     model   vdw
     2.393 3.120
  nonbonded pdb=" OD1 ASP C 146 "
            pdb=" ND2 ASN C 172 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" N   ASP C 251 "
            pdb=" OD1 ASP C 251 "
     model   vdw
     2.428 3.120
  ... (remaining 32842 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.230
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
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   0.032   4720  Z= 0.151
  Angle     :  0.531   9.385   6432  Z= 0.262
  Chirality :  0.042   0.357    746
  Planarity :  0.003   0.027    802
  Dihedral  : 22.682 108.587   1943
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.76 (0.33), residues: 543
  helix:  2.07 (0.45), residues: 130
  sheet: -1.48 (0.37), residues: 170
  loop : -2.82 (0.28), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.006   0.001   TYR A 183 
 PHE   0.005   0.001   PHE A 120 
 TRP   0.003   0.001   TRP C 293 
 HIS   0.003   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4700)
  covalent geometry    : angle       0.51127 ( 6379)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.52330 (   14)
  hydrogen bonds       : bond        0.19015 (  180)
  hydrogen bonds       : angle       6.57776 (  525)
  link_BETA1-4         : bond        0.00346 (    5)
  link_BETA1-4         : angle       0.85718 (   15)
  link_NAG-ASN         : bond        0.00472 (    8)
  link_NAG-ASN         : angle       2.35438 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8007 (tm-30)
REVERT: A  149 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5463 (mp0)
REVERT: C  245 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7468 (tpm170)
  outliers start: 1
  outliers final: 1
  residues processed: 90
  average time/residue: 0.0745
  time to fit residues: 8.2693
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN
A  61 ASN
B 269 GLN
C 171 GLN
C 286 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.118539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097757 restraints weight = 7599.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 3.01
r_work: 0.3123 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4720  Z= 0.167
  Angle     :  0.741   9.937   6432  Z= 0.321
  Chirality :  0.047   0.250    746
  Planarity :  0.004   0.036    802
  Dihedral  : 24.180 109.879    868
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.01 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.35), residues: 543
  helix:  2.92 (0.45), residues: 130
  sheet: -0.97 (0.38), residues: 175
  loop : -2.40 (0.34), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 185 
 TYR   0.016   0.002   TYR A 105 
 PHE   0.010   0.002   PHE A 114 
 TRP   0.015   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4700)
  covalent geometry    : angle       0.70120 ( 6379)
  SS BOND              : bond        0.00212 (    7)
  SS BOND              : angle       1.10207 (   14)
  hydrogen bonds       : bond        0.04751 (  180)
  hydrogen bonds       : angle       4.73632 (  525)
  link_BETA1-4         : bond        0.00401 (    5)
  link_BETA1-4         : angle       2.02763 (   15)
  link_NAG-ASN         : bond        0.00373 (    8)
  link_NAG-ASN         : angle       3.62749 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8542 (tm-30)
REVERT: A  149 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5566 (mp0)
REVERT: C  215 GLN cc_start: 0.8084 (tt0) cc_final: 0.7853 (tt0)
REVERT: C  245 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7405 (tpm170)
REVERT: C  276 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7617 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0468
  time to fit residues: 4.4726
Evaluate side-chains
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 269 GLN
C 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.095175 restraints weight = 7529.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.92
r_work: 0.3083 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4720  Z= 0.140
  Angle     :  0.708   9.320   6432  Z= 0.306
  Chirality :  0.047   0.242    746
  Planarity :  0.004   0.038    802
  Dihedral  : 18.824 116.914    868
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.37 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.36), residues: 543
  helix:  3.41 (0.45), residues: 130
  sheet: -0.74 (0.38), residues: 174
  loop : -2.13 (0.35), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 265 
 TYR   0.011   0.001   TYR B 224 
 PHE   0.011   0.001   PHE A 114 
 TRP   0.014   0.001   TRP C 293 
 HIS   0.002   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4700)
  covalent geometry    : angle       0.68324 ( 6379)
  SS BOND              : bond        0.00270 (    7)
  SS BOND              : angle       0.99192 (   14)
  hydrogen bonds       : bond        0.04420 (  180)
  hydrogen bonds       : angle       4.27156 (  525)
  link_BETA1-4         : bond        0.00554 (    5)
  link_BETA1-4         : angle       2.04891 (   15)
  link_NAG-ASN         : bond        0.01093 (    8)
  link_NAG-ASN         : angle       2.63125 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7222 (tp)
REVERT: A  149 GLU cc_start: 0.5883 (mm-30) cc_final: 0.5600 (mp0)
REVERT: C  245 ARG cc_start: 0.8420 (tpp80) cc_final: 0.7344 (tpm170)
REVERT: C  276 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8150 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0520
  time to fit residues: 4.5692
Evaluate side-chains
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.088245 restraints weight = 7773.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.96
r_work: 0.2969 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4720  Z= 0.213
  Angle     :  0.818  11.863   6432  Z= 0.359
  Chirality :  0.050   0.279    746
  Planarity :  0.004   0.035    802
  Dihedral  : 14.602  90.899    868
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.96 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.37), residues: 543
  helix:  3.33 (0.45), residues: 130
  sheet: -0.61 (0.38), residues: 173
  loop : -2.12 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 327 
 TYR   0.017   0.002   TYR A 183 
 PHE   0.018   0.002   PHE A 114 
 TRP   0.017   0.002   TRP C 293 
 HIS   0.004   0.001   HIS C 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 4700)
  covalent geometry    : angle       0.77706 ( 6379)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       1.29959 (   14)
  hydrogen bonds       : bond        0.06335 (  180)
  hydrogen bonds       : angle       4.59731 (  525)
  link_BETA1-4         : bond        0.00533 (    5)
  link_BETA1-4         : angle       2.40443 (   15)
  link_NAG-ASN         : bond        0.01018 (    8)
  link_NAG-ASN         : angle       3.74835 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7482 (tp)
REVERT: A  149 GLU cc_start: 0.5946 (mm-30) cc_final: 0.5724 (mp0)
REVERT: C  267 GLN cc_start: 0.8015 (tt0) cc_final: 0.7807 (tt0)
REVERT: C  276 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: C  327 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.5673 (mmp-170)
  outliers start: 15
  outliers final: 12
  residues processed: 59
  average time/residue: 0.0655
  time to fit residues: 5.3084
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0060
   chunk 7 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.092501 restraints weight = 7605.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.95
r_work: 0.3036 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4720  Z= 0.117
  Angle     :  0.688  10.455   6432  Z= 0.299
  Chirality :  0.044   0.245    746
  Planarity :  0.003   0.038    802
  Dihedral  : 13.212  96.164    868
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.13 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.38), residues: 543
  helix:  3.71 (0.46), residues: 130
  sheet: -0.49 (0.39), residues: 176
  loop : -1.85 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.010   0.001   TYR A  97 
 PHE   0.009   0.001   PHE C 322 
 TRP   0.008   0.001   TRP C 293 
 HIS   0.001   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4700)
  covalent geometry    : angle       0.65777 ( 6379)
  SS BOND              : bond        0.00343 (    7)
  SS BOND              : angle       0.83675 (   14)
  hydrogen bonds       : bond        0.04292 (  180)
  hydrogen bonds       : angle       4.09725 (  525)
  link_BETA1-4         : bond        0.00720 (    5)
  link_BETA1-4         : angle       2.50921 (   15)
  link_NAG-ASN         : bond        0.00755 (    8)
  link_NAG-ASN         : angle       2.73240 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7346 (tp)
REVERT: A  149 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5633 (mp0)
REVERT: B  232 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (mp0)
REVERT: C  276 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: C  327 ARG cc_start: 0.6596 (mtt-85) cc_final: 0.5362 (mmp-170)
  outliers start: 9
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0496
  time to fit residues: 3.6196
Evaluate side-chains
  49 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.111165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.090656 restraints weight = 7789.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.99
r_work: 0.3003 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4720  Z= 0.139
  Angle     :  0.700  13.105   6432  Z= 0.304
  Chirality :  0.044   0.220    746
  Planarity :  0.003   0.035    802
  Dihedral  : 11.709  90.010    868
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.72 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.37), residues: 543
  helix:  3.77 (0.45), residues: 130
  sheet: -0.28 (0.40), residues: 173
  loop : -1.76 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 327 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 114 
 TRP   0.009   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4700)
  covalent geometry    : angle       0.66628 ( 6379)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       0.97426 (   14)
  hydrogen bonds       : bond        0.04755 (  180)
  hydrogen bonds       : angle       4.10923 (  525)
  link_BETA1-4         : bond        0.00715 (    5)
  link_BETA1-4         : angle       2.58211 (   15)
  link_NAG-ASN         : bond        0.00713 (    8)
  link_NAG-ASN         : angle       2.93819 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7416 (tp)
REVERT: A  149 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5692 (mp0)
REVERT: B  215 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8824 (p)
REVERT: C  276 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7934 (tm-30)
REVERT: C  327 ARG cc_start: 0.6408 (mtt-85) cc_final: 0.5281 (mmp-170)
  outliers start: 14
  outliers final: 10
  residues processed: 55
  average time/residue: 0.0551
  time to fit residues: 4.2428
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 34 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0370
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.093586 restraints weight = 7628.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.96
r_work: 0.3056 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4720  Z= 0.105
  Angle     :  0.649  13.416   6432  Z= 0.284
  Chirality :  0.043   0.221    746
  Planarity :  0.003   0.036    802
  Dihedral  : 10.688  89.033    868
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.11 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.38), residues: 543
  helix:  3.93 (0.45), residues: 130
  sheet: -0.34 (0.39), residues: 176
  loop : -1.55 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.008   0.001   TYR A  97 
 PHE   0.008   0.001   PHE B 295 
 TRP   0.008   0.001   TRP A 181 
 HIS   0.001   0.000   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4700)
  covalent geometry    : angle       0.61818 ( 6379)
  SS BOND              : bond        0.00178 (    7)
  SS BOND              : angle       0.82356 (   14)
  hydrogen bonds       : bond        0.03641 (  180)
  hydrogen bonds       : angle       3.83015 (  525)
  link_BETA1-4         : bond        0.00834 (    5)
  link_BETA1-4         : angle       2.61272 (   15)
  link_NAG-ASN         : bond        0.00610 (    8)
  link_NAG-ASN         : angle       2.59150 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7330 (tp)
REVERT: A  149 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5673 (mp0)
REVERT: C  276 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: C  327 ARG cc_start: 0.6425 (mtt-85) cc_final: 0.5238 (mmp-170)
  outliers start: 13
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0541
  time to fit residues: 4.5686
Evaluate side-chains
  52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.111385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.092211 restraints weight = 7727.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.59
r_work: 0.3030 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4720  Z= 0.137
  Angle     :  0.668  13.884   6432  Z= 0.295
  Chirality :  0.044   0.217    746
  Planarity :  0.003   0.034    802
  Dihedral  : 10.283  85.357    868
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.52 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.38), residues: 543
  helix:  3.94 (0.44), residues: 130
  sheet: -0.31 (0.39), residues: 175
  loop : -1.53 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 327 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.010   0.001   PHE A 114 
 TRP   0.007   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4700)
  covalent geometry    : angle       0.63695 ( 6379)
  SS BOND              : bond        0.00260 (    7)
  SS BOND              : angle       1.00104 (   14)
  hydrogen bonds       : bond        0.04549 (  180)
  hydrogen bonds       : angle       3.94835 (  525)
  link_BETA1-4         : bond        0.00784 (    5)
  link_BETA1-4         : angle       2.53053 (   15)
  link_NAG-ASN         : bond        0.00640 (    8)
  link_NAG-ASN         : angle       2.65239 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7427 (tp)
REVERT: A  149 GLU cc_start: 0.5958 (mm-30) cc_final: 0.5756 (mp0)
REVERT: B  215 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8783 (p)
REVERT: C  267 GLN cc_start: 0.8048 (tt0) cc_final: 0.7805 (tt0)
REVERT: C  276 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: C  327 ARG cc_start: 0.6484 (mtt-85) cc_final: 0.5249 (mmp-170)
  outliers start: 13
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0549
  time to fit residues: 4.1495
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.093168 restraints weight = 7602.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.56
r_work: 0.3046 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4720  Z= 0.122
  Angle     :  0.659  14.574   6432  Z= 0.295
  Chirality :  0.043   0.217    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.955  83.364    868
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.11 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.38), residues: 543
  helix:  4.02 (0.44), residues: 130
  sheet: -0.34 (0.39), residues: 176
  loop : -1.41 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 327 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.009   0.001   PHE A 114 
 TRP   0.014   0.001   TRP B 308 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4700)
  covalent geometry    : angle       0.63108 ( 6379)
  SS BOND              : bond        0.00205 (    7)
  SS BOND              : angle       0.94771 (   14)
  hydrogen bonds       : bond        0.04192 (  180)
  hydrogen bonds       : angle       3.89364 (  525)
  link_BETA1-4         : bond        0.00830 (    5)
  link_BETA1-4         : angle       2.45911 (   15)
  link_NAG-ASN         : bond        0.00568 (    8)
  link_NAG-ASN         : angle       2.48972 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7391 (tp)
REVERT: C  276 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: C  327 ARG cc_start: 0.6490 (mtt-85) cc_final: 0.5208 (mmp-170)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.0560
  time to fit residues: 3.9259
Evaluate side-chains
  51 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0050
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.113994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.094866 restraints weight = 7621.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.59
r_work: 0.3072 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4720  Z= 0.105
  Angle     :  0.643  14.800   6432  Z= 0.288
  Chirality :  0.043   0.207    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.588  79.215    868
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.91 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.38), residues: 543
  helix:  4.11 (0.44), residues: 130
  sheet: -0.25 (0.39), residues: 175
  loop : -1.33 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 260 
 TYR   0.008   0.001   TYR A 183 
 PHE   0.008   0.001   PHE C 305 
 TRP   0.009   0.001   TRP B 308 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 4700)
  covalent geometry    : angle       0.61625 ( 6379)
  SS BOND              : bond        0.00169 (    7)
  SS BOND              : angle       0.85056 (   14)
  hydrogen bonds       : bond        0.03561 (  180)
  hydrogen bonds       : angle       3.74881 (  525)
  link_BETA1-4         : bond        0.00815 (    5)
  link_BETA1-4         : angle       2.37127 (   15)
  link_NAG-ASN         : bond        0.00513 (    8)
  link_NAG-ASN         : angle       2.41343 (   24)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7312 (tp)
REVERT: B  215 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (p)
REVERT: C  267 GLN cc_start: 0.7959 (tt0) cc_final: 0.7722 (tt0)
REVERT: C  276 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: C  327 ARG cc_start: 0.6505 (mtt-85) cc_final: 0.5131 (mmp-170)
  outliers start: 11
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0528
  time to fit residues: 4.1241
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  282 CYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  319 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.113486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.094410 restraints weight = 7634.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.58
r_work: 0.3066 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4720  Z= 0.112
  Angle     :  0.642  14.798   6432  Z= 0.288
  Chirality :  0.043   0.203    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.486  76.513    868
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.72 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.38), residues: 543
  helix:  4.19 (0.44), residues: 130
  sheet: -0.23 (0.39), residues: 174
  loop : -1.23 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 327 
 TYR   0.009   0.001   TYR A 183 
 PHE   0.009   0.001   PHE C 305 
 TRP   0.010   0.001   TRP B 308 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4700)
  covalent geometry    : angle       0.61622 ( 6379)
  SS BOND              : bond        0.00228 (    7)
  SS BOND              : angle       0.90214 (   14)
  hydrogen bonds       : bond        0.03794 (  180)
  hydrogen bonds       : angle       3.78510 (  525)
  link_BETA1-4         : bond        0.00801 (    5)
  link_BETA1-4         : angle       2.26007 (   15)
  link_NAG-ASN         : bond        0.00527 (    8)
  link_NAG-ASN         : angle       2.42970 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1169.68 seconds
wall clock time: 20 minutes 41.25 seconds (1241.25 seconds total)