Starting phenix.real_space_refine
on Tue Jan 14 00:05:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2c_42905/01_2025/8v2c_42905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2c_42905/01_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_42905/01_2025/8v2c_42905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2c_42905/01_2025/8v2c_42905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2c_42905/01_2025/8v2c_42905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2c_42905/01_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-5571/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: 3.72, per 1000 atoms: 0.81
  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: 1.19
  Conformation dependent library (CDL) restraints added in 483.2 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: 0.45
  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: 0.98

  Time building geometry restraints manager: 1.32 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:             2.010
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.400
  Find NCS groups from input model:        0.080
  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:2.600
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.390
-------------------------------------------------------------------------------
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  : 0.525 
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: 0.1970
  time to fit residues: 21.9041
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  : 0.532 
-------------------------------------------------------------------------------
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:    0.4980
   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 = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.104956 restraints weight = 7508.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.99
r_work: 0.3235 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    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 = 0.3217 r_free = 0.3217    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
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= 0.139
  Angle     :  0.631   9.245   6379  Z= 0.277
  Chirality :  0.047   0.317    746
  Planarity :  0.004   0.041    802
  Dihedral  : 24.451 113.755    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  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: A  149 GLU cc_start: 0.5832 (mm-30) cc_final: 0.5471 (mp0)
REVERT: C  245 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7396 (tpm170)
REVERT: C  276 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: C  294 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6889 (mm-40)
  outliers start: 8
  outliers final: 3
  residues processed: 72
  average time/residue: 0.1337
  time to fit residues: 13.0767
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  : 0.524 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0870
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.119715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098907 restraints weight = 7505.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 3.01
r_work: 0.3142 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4700  Z= 0.177
  Angle     :  0.664  10.852   6379  Z= 0.291
  Chirality :  0.046   0.241    746
  Planarity :  0.003   0.037    802
  Dihedral  : 19.323 116.252    868
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.60 %
    Favored  : 85.43 %
  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: -0.28 (0.37), residues: 543
  helix:  3.50 (0.45), residues: 130
  sheet: -0.66 (0.38), residues: 176
  loop : -2.01 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 293 
 HIS   0.002   0.001   HIS C 193 
 PHE   0.009   0.001   PHE A 114 
 TYR   0.011   0.001   TYR B 224 
 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
  67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: A  144 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7097 (tp)
REVERT: A  149 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5539 (mp0)
REVERT: C  215 GLN cc_start: 0.8082 (tt0) cc_final: 0.7813 (tt0)
REVERT: C  245 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7416 (tpm170)
REVERT: C  294 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6858 (mm-40)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1272
  time to fit residues: 11.4654
Evaluate side-chains
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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 C residue  185 ILE
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  275 CYS
Chi-restraints excluded: chain C residue  282 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.114395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.093717 restraints weight = 7586.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.96
r_work: 0.3055 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    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 = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2518

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= 0.225
  Angle     :  0.694  10.764   6379  Z= 0.304
  Chirality :  0.048   0.295    746
  Planarity :  0.004   0.039    802
  Dihedral  : 14.907  94.960    868
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.37 %
    Favored  : 83.07 %
  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: -0.13 (0.37), residues: 543
  helix:  3.62 (0.45), residues: 130
  sheet: -0.49 (0.38), residues: 176
  loop : -1.98 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 293 
 HIS   0.003   0.001   HIS C 326 
 PHE   0.012   0.002   PHE A 114 
 TYR   0.014   0.002   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
  67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7320 (tp)
REVERT: A  149 GLU cc_start: 0.5899 (mm-30) cc_final: 0.5632 (mp0)
REVERT: C  245 ARG cc_start: 0.8417 (tpp80) cc_final: 0.7338 (tpm170)
  outliers start: 13
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1233
  time to fit residues: 11.0336
Evaluate side-chains
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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  185 ILE
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 6 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.086274 restraints weight = 7960.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 3.00
r_work: 0.2927 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   4700  Z= 0.410
  Angle     :  0.808  12.841   6379  Z= 0.376
  Chirality :  0.049   0.262    746
  Planarity :  0.005   0.035    802
  Dihedral  : 12.852  95.881    868
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.75 %
    Favored  : 81.50 %
  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: -0.32 (0.37), residues: 543
  helix:  3.25 (0.45), residues: 130
  sheet: -0.56 (0.39), residues: 174
  loop : -1.99 (0.36), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 293 
 HIS   0.004   0.001   HIS C 326 
 PHE   0.020   0.003   PHE A 114 
 TYR   0.021   0.003   TYR A 183 
 ARG   0.008   0.001   ARG C 327 

*********************** 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
  58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7584 (tp)
REVERT: A  195 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7328 (mtm110)
  outliers start: 14
  outliers final: 11
  residues processed: 56
  average time/residue: 0.1449
  time to fit residues: 11.0768
Evaluate side-chains
  51 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0070
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0010
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4404

-------------------------------------------------------------------------------
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 = 0.3434 r_free = 0.3434 target = 0.111804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.091352 restraints weight = 7590.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.97
r_work: 0.3018 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4700  Z= 0.168
  Angle     :  0.663  12.796   6379  Z= 0.296
  Chirality :  0.044   0.221    746
  Planarity :  0.004   0.038    802
  Dihedral  : 11.666  90.704    868
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.34 %
    Favored  : 81.30 %
  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:  0.04 (0.38), residues: 543
  helix:  3.73 (0.46), residues: 130
  sheet: -0.52 (0.39), residues: 176
  loop : -1.74 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 293 
 HIS   0.001   0.000   HIS A  91 
 PHE   0.010   0.001   PHE C 322 
 TYR   0.011   0.001   TYR A  97 
 ARG   0.002   0.000   ARG A 185 

*********************** 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
  51 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7453 (tp)
  outliers start: 12
  outliers final: 7
  residues processed: 49
  average time/residue: 0.1093
  time to fit residues: 8.0232
Evaluate side-chains
  46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  234 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    0.0670
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3430 r_free = 0.3430 target = 0.112637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.093797 restraints weight = 7490.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.54
r_work: 0.3056 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    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 = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4700  Z= 0.167
  Angle     :  0.629  13.183   6379  Z= 0.284
  Chirality :  0.043   0.222    746
  Planarity :  0.003   0.036    802
  Dihedral  : 10.541  88.250    868
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.73 %
    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:  0.23 (0.38), residues: 543
  helix:  3.89 (0.45), residues: 130
  sheet: -0.44 (0.38), residues: 175
  loop : -1.59 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 181 
 HIS   0.002   0.000   HIS A 146 
 PHE   0.009   0.001   PHE A 114 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.001   0.000   ARG C 245 

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7361 (tp)
REVERT: A  195 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6871 (ttm170)
REVERT: B  215 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8752 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 56
  average time/residue: 0.1252
  time to fit residues: 9.9172
Evaluate side-chains
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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 B residue  215 VAL
Chi-restraints excluded: chain B residue  234 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 41 optimal weight:    0.0770
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN
C 189 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.114357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.095571 restraints weight = 7503.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.53
r_work: 0.3086 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.3486

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= 0.134
  Angle     :  0.604  14.294   6379  Z= 0.273
  Chirality :  0.042   0.213    746
  Planarity :  0.003   0.035    802
  Dihedral  : 10.076  85.702    868
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.13 %
    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 (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:  0.38 (0.38), residues: 543
  helix:  4.02 (0.45), residues: 130
  sheet: -0.40 (0.38), residues: 176
  loop : -1.46 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 181 
 HIS   0.001   0.000   HIS C 326 
 PHE   0.008   0.001   PHE B 295 
 TYR   0.008   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 185 

*********************** 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
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7257 (tp)
REVERT: A  195 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6812 (ttp-110)
REVERT: B  215 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1223
  time to fit residues: 10.0591
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
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 0 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0970
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.113269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.094327 restraints weight = 7571.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.55
r_work: 0.3065 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
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:        9 |
|-----------------------------------------------------------------------------|
|-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:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4700  Z= 0.158
  Angle     :  0.612  14.272   6379  Z= 0.280
  Chirality :  0.043   0.210    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.777  82.346    868
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.93 %
    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 (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 (0.38), residues: 543
  helix:  4.07 (0.45), residues: 130
  sheet: -0.42 (0.38), residues: 176
  loop : -1.35 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 181 
 HIS   0.002   0.000   HIS A 146 
 PHE   0.009   0.001   PHE C 305 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.002   0.000   ARG B 260 

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7299 (tp)
REVERT: A  195 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6955 (ttp-110)
REVERT: B  215 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8729 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 56
  average time/residue: 0.1228
  time to fit residues: 9.7023
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  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
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  234 LEU
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 6 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.110696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.091735 restraints weight = 7521.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.55
r_work: 0.3023 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4700  Z= 0.214
  Angle     :  0.636  14.790   6379  Z= 0.293
  Chirality :  0.044   0.210    746
  Planarity :  0.004   0.034    802
  Dihedral  :  9.669  78.335    868
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  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:  0.40 (0.38), residues: 543
  helix:  3.97 (0.44), residues: 130
  sheet: -0.37 (0.38), residues: 176
  loop : -1.40 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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   0.002   0.000   ARG A  68 

********************** 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
  54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7405 (tp)
REVERT: A  195 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.6961 (ttm170)
  outliers start: 14
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1365
  time to fit residues: 9.8300
Evaluate side-chains
  52 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
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  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:    0.9980
   chunk 39 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.112730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.093743 restraints weight = 7520.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.56
r_work: 0.3055 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
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:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4700  Z= 0.157
  Angle     :  0.610  14.546   6379  Z= 0.280
  Chirality :  0.043   0.204    746
  Planarity :  0.003   0.035    802
  Dihedral  :  9.435  75.436    868
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  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 (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:  0.50 (0.38), residues: 543
  helix:  4.04 (0.45), residues: 130
  sheet: -0.33 (0.38), residues: 176
  loop : -1.32 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 195 
 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   0.001   0.000   ARG B 260 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2549.17 seconds
wall clock time: 45 minutes 53.94 seconds (2753.94 seconds total)