Starting phenix.real_space_refine
on Thu Mar  6 03:08:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2c_42905/03_2025/8v2c_42905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2c_42905/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v2c_42905/03_2025/8v2c_42905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2c_42905/03_2025/8v2c_42905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2c_42905/03_2025/8v2c_42905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2c_42905/03_2025/8v2c_42905.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.08, per 1000 atoms: 0.89
  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: 1.28
  Conformation dependent library (CDL) restraints added in 524.2 milliseconds
  

  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: 0.46
  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: 1.11

  Time building geometry restraints manager: 1.45 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:             3.620
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.770
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.730
-------------------------------------------------------------------------------
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   4700  Z= 0.192
  Angle     :  0.511   6.325   6379  Z= 0.258
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP C 293 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.005   0.001   PHE A 120 
 TYR   0.006   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 134 

*********************** 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  : 0.545 
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: 0.2210
  time to fit residues: 24.4440
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  : 0.546 
-------------------------------------------------------------------------------
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 44 optimal weight:    0.0040
   chunk 40 optimal weight:    0.0870
   chunk 22 optimal weight:    0.2980
   chunk 13 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0980
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.1370

-------------------------------------------------------------------------------
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 176 HIS
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 = 0.3628 r_free = 0.3628 target = 0.125622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.104897 restraints weight = 7508.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 3.00
r_work: 0.3234 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4700  Z= 0.138
  Angle     :  0.631   9.255   6379  Z= 0.277
  Chirality :  0.047   0.317    746
  Planarity :  0.004   0.041    802
  Dihedral  : 24.456 113.718    868
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.63 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.36), residues: 543
  helix:  3.09 (0.45), residues: 130
  sheet: -0.96 (0.37), residues: 174
  loop : -2.29 (0.34), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 293 
 HIS   0.003   0.001   HIS A  74 
 PHE   0.007   0.001   PHE C 305 
 TYR   0.015   0.001   TYR A 105 
 ARG   0.002   0.000   ARG A 185 

*********************** 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
  75 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8513 (tm-30)
REVERT: A  149 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5467 (mp0)
REVERT: C  245 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7399 (tpm170)
REVERT: C  276 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: C  294 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6892 (mm-40)
  outliers start: 8
  outliers final: 3
  residues processed: 72
  average time/residue: 0.1380
  time to fit residues: 13.5124
Evaluate side-chains
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain C residue  275 CYS
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 33 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.116383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095552 restraints weight = 7546.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 3.01
r_work: 0.3091 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4700  Z= 0.226
  Angle     :  0.697  11.706   6379  Z= 0.308
  Chirality :  0.047   0.245    746
  Planarity :  0.004   0.036    802
  Dihedral  : 18.834 114.593    868
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.60 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.36), residues: 543
  helix:  3.43 (0.45), residues: 130
  sheet: -0.79 (0.38), residues: 178
  loop : -2.13 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 293 
 HIS   0.002   0.001   HIS C 193 
 PHE   0.012   0.002   PHE A 114 
 TYR   0.014   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 185 

*********************** 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
  66 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7203 (tp)
REVERT: A  149 GLU cc_start: 0.5870 (mm-30) cc_final: 0.5556 (mp0)
REVERT: C  215 GLN cc_start: 0.8133 (tt0) cc_final: 0.7863 (tt0)
REVERT: C  245 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7407 (tpm170)
REVERT: C  276 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8117 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 64
  average time/residue: 0.1235
  time to fit residues: 11.1894
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  185 ILE
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.114472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.093908 restraints weight = 7570.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.96
r_work: 0.3058 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4700  Z= 0.209
  Angle     :  0.690  11.185   6379  Z= 0.301
  Chirality :  0.047   0.282    746
  Planarity :  0.004   0.039    802
  Dihedral  : 14.417  93.872    868
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.96 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.37), residues: 543
  helix:  3.66 (0.45), residues: 130
  sheet: -0.49 (0.38), residues: 176
  loop : -1.94 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 293 
 HIS   0.002   0.001   HIS C 326 
 PHE   0.011   0.002   PHE A 114 
 TYR   0.013   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8878 (tp30) cc_final: 0.8466 (tm-30)
REVERT: A  144 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7284 (tp)
REVERT: A  149 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5636 (mp0)
REVERT: A  196 GLU cc_start: 0.7700 (tp30) cc_final: 0.7445 (tp30)
REVERT: C  245 ARG cc_start: 0.8443 (tpp80) cc_final: 0.7367 (tpm170)
REVERT: C  276 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: C  327 ARG cc_start: 0.7318 (mtt-85) cc_final: 0.5572 (mmp-170)
  outliers start: 9
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1535
  time to fit residues: 12.0918
Evaluate side-chains
  52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  145 GLN
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  319 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0060
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.115043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.094530 restraints weight = 7687.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.98
r_work: 0.3069 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4700  Z= 0.161
  Angle     :  0.646   9.990   6379  Z= 0.283
  Chirality :  0.044   0.235    746
  Planarity :  0.003   0.035    802
  Dihedral  : 12.913  97.271    868
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.16 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.37), residues: 543
  helix:  3.78 (0.45), residues: 130
  sheet: -0.38 (0.39), residues: 174
  loop : -1.82 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 293 
 HIS   0.001   0.000   HIS C 193 
 PHE   0.010   0.001   PHE A 114 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.005   0.000   ARG C 222 

*********************** 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
  62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7279 (tp)
REVERT: A  149 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5605 (mp0)
REVERT: B  250 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9017 (tt)
REVERT: C  245 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7292 (tpm170)
REVERT: C  276 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: C  327 ARG cc_start: 0.7284 (mtt-85) cc_final: 0.5548 (mmp-170)
  outliers start: 13
  outliers final: 10
  residues processed: 59
  average time/residue: 0.1536
  time to fit residues: 12.1806
Evaluate side-chains
  58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  250 LEU
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  319 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.114058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.093551 restraints weight = 7548.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.96
r_work: 0.3052 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4700  Z= 0.184
  Angle     :  0.656  12.486   6379  Z= 0.289
  Chirality :  0.044   0.218    746
  Planarity :  0.003   0.034    802
  Dihedral  : 11.422  91.201    868
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.37), residues: 543
  helix:  3.86 (0.45), residues: 130
  sheet: -0.28 (0.39), residues: 172
  loop : -1.67 (0.37), residues: 241

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

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7347 (tp)
REVERT: A  149 GLU cc_start: 0.5831 (mm-30) cc_final: 0.5600 (mp0)
REVERT: C  327 ARG cc_start: 0.6909 (mtt-85) cc_final: 0.5419 (mmp-170)
  outliers start: 12
  outliers final: 10
  residues processed: 57
  average time/residue: 0.1267
  time to fit residues: 10.2106
Evaluate side-chains
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  319 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    0.0040
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0770
   chunk 46 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5152

-------------------------------------------------------------------------------
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 = 0.3475 r_free = 0.3475 target = 0.114905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.094431 restraints weight = 7500.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.95
r_work: 0.3065 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4700  Z= 0.162
  Angle     :  0.630  13.403   6379  Z= 0.280
  Chirality :  0.043   0.224    746
  Planarity :  0.003   0.034    802
  Dihedral  : 10.415  89.033    868
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.73 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.38), residues: 543
  helix:  3.94 (0.45), residues: 130
  sheet: -0.27 (0.39), residues: 174
  loop : -1.54 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 293 
 HIS   0.001   0.000   HIS A 146 
 PHE   0.008   0.001   PHE A 114 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.002   0.000   ARG C 327 

*********************** 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
  63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7296 (tp)
REVERT: A  149 GLU cc_start: 0.5843 (mm-30) cc_final: 0.5611 (mp0)
REVERT: C  276 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: C  327 ARG cc_start: 0.6352 (mtt-85) cc_final: 0.5144 (mmp-170)
  outliers start: 13
  outliers final: 9
  residues processed: 60
  average time/residue: 0.1189
  time to fit residues: 10.1592
Evaluate side-chains
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
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 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0970
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.112794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.093666 restraints weight = 7525.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.56
r_work: 0.3053 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4700  Z= 0.195
  Angle     :  0.635  14.224   6379  Z= 0.286
  Chirality :  0.043   0.216    746
  Planarity :  0.003   0.033    802
  Dihedral  :  9.976  84.142    868
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.93 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.38), residues: 543
  helix:  3.91 (0.44), residues: 130
  sheet: -0.36 (0.39), residues: 176
  loop : -1.45 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.010   0.001   PHE A 114 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

*********************** 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
  62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7317 (tp)
REVERT: A  149 GLU cc_start: 0.5954 (mm-30) cc_final: 0.5728 (mp0)
REVERT: A  195 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6962 (ttp-110)
REVERT: C  276 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: C  327 ARG cc_start: 0.6435 (mtt-85) cc_final: 0.5242 (mmp-170)
  outliers start: 14
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1327
  time to fit residues: 10.8290
Evaluate side-chains
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue  117 THR
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 189 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.111667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.092443 restraints weight = 7601.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.57
r_work: 0.3035 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4700  Z= 0.219
  Angle     :  0.652  14.723   6379  Z= 0.298
  Chirality :  0.044   0.216    746
  Planarity :  0.003   0.034    802
  Dihedral  :  9.778  81.560    868
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.38), residues: 543
  helix:  3.95 (0.44), residues: 130
  sheet: -0.37 (0.39), residues: 176
  loop : -1.40 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.011   0.001   PHE A 114 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

*********************** 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
  57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7405 (tp)
REVERT: A  149 GLU cc_start: 0.6005 (mm-30) cc_final: 0.5800 (mp0)
REVERT: C  276 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: C  327 ARG cc_start: 0.6524 (mtt-85) cc_final: 0.5316 (mmp-170)
  outliers start: 14
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1257
  time to fit residues: 9.5235
Evaluate side-chains
  53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 6 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.112292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.093185 restraints weight = 7492.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.55
r_work: 0.3046 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4700  Z= 0.189
  Angle     :  0.642  14.972   6379  Z= 0.293
  Chirality :  0.044   0.212    746
  Planarity :  0.004   0.034    802
  Dihedral  :  9.607  78.924    868
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.38), residues: 543
  helix:  3.97 (0.44), residues: 130
  sheet: -0.32 (0.39), residues: 176
  loop : -1.33 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 293 
 HIS   0.002   0.000   HIS A 146 
 PHE   0.010   0.001   PHE A 114 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.003   0.000   ARG C 327 

********************** 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
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7405 (tp)
REVERT: A  149 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5762 (mp0)
REVERT: C  276 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: C  327 ARG cc_start: 0.6533 (mtt-85) cc_final: 0.5323 (mmp-170)
  outliers start: 12
  outliers final: 11
  residues processed: 52
  average time/residue: 0.1373
  time to fit residues: 9.9898
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.111367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.092302 restraints weight = 7559.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.55
r_work: 0.3031 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4700  Z= 0.217
  Angle     :  0.648  14.817   6379  Z= 0.296
  Chirality :  0.044   0.207    746
  Planarity :  0.004   0.034    802
  Dihedral  :  9.524  75.408    868
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.38), residues: 543
  helix:  3.97 (0.44), residues: 130
  sheet: -0.32 (0.39), residues: 176
  loop : -1.34 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 293 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.011   0.001   PHE A 114 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.004   0.000   ARG C 327 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2473.43 seconds
wall clock time: 43 minutes 13.77 seconds (2593.77 seconds total)