Starting phenix.real_space_refine
on Tue Mar  3 14:39:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2026/7p5m_13201.cif"
  }
  resolution = 3.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      46      5.16       5
     C    4006      2.51       5
     N     976      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6204
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    Chain: "C"
      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: "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: "A"
      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
  Time building chain proxies: 1.50, per 1000 atoms: 0.24
  Number of scatterers: 6204
  At special positions: 0
  Unit cell: (92.442, 70.308, 128.898, 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      46     16.00
     O    1176      8.00
     N     976      7.00
     C    4006      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " 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 C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 247.0 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 18
    Processing helix  chain 'A' and resid 38 through 70
      removed outlier: 3.660A  pdb=" N   ALA A  70 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 159
      removed outlier: 4.199A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.333A  pdb=" N   ALA A 163 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 191 through 237
      removed outlier: 3.502A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.654A  pdb=" N   LEU A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 300
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.971A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 382
      removed outlier: 4.426A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 414
      removed outlier: 3.682A  pdb=" N   GLN A 387 " --> pdb=" O   TYR A 383 " (cutoff:3.500A)
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 70
      removed outlier: 3.646A  pdb=" N   ALA B  70 " --> pdb=" O   TYR B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 159
      removed outlier: 4.245A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 4.284A  pdb=" N   ALA B 163 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 187
    Processing helix  chain 'B' and resid 191 through 237
      removed outlier: 3.611A  pdb=" N   LEU B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 276
      removed outlier: 3.739A  pdb=" N   LEU B 242 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER B 244 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 4.127A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 341 through 365
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.418A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 409
      removed outlier: 3.543A  pdb=" N   GLN B 387 " --> pdb=" O   TYR B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 414

    562 hydrogen bonds defined for protein.
    1680 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: 0.99

  Time building geometry restraints manager: 0.90 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: 1918
        1.34 -     1.46: 1290
        1.46 -     1.58: 3062
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6332
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  ... (remaining 6327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 8391
        1.59 -     3.19: 201
        3.19 -     4.78: 25
        4.78 -     6.37: 8
        6.37 -     7.97: 5
  Bond angle restraints: 8630
  Sorted by residual:
  angle pdb=" C   LEU B 282 "
        pdb=" N   ASN B 283 "
        pdb=" CA  ASN B 283 "
      ideal   model   delta    sigma   weight residual
     122.65  116.56    6.09 1.60e+00 3.91e-01 1.45e+01
  angle pdb=" C   ASP B 166 "
        pdb=" N   TYR B 167 "
        pdb=" CA  TYR B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   ASP A 166 "
        pdb=" N   TYR A 167 "
        pdb=" CA  TYR A 167 "
      ideal   model   delta    sigma   weight residual
     121.54  127.82   -6.28 1.91e+00 2.74e-01 1.08e+01
  angle pdb=" C   LEU A 282 "
        pdb=" N   ASN A 283 "
        pdb=" CA  ASN A 283 "
      ideal   model   delta    sigma   weight residual
     122.38  116.47    5.91 1.81e+00 3.05e-01 1.07e+01
  angle pdb=" N   VAL B  23 "
        pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     113.71  110.95    2.76 9.50e-01 1.11e+00 8.42e+00
  ... (remaining 8625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.30: 3538
       21.30 -    42.59: 249
       42.59 -    63.89: 39
       63.89 -    85.18: 6
       85.18 -   106.48: 16
  Dihedral angle restraints: 3848
    sinusoidal: 1562
      harmonic: 2286
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.58   31.42     1      1.00e+01 1.00e-02 1.41e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.63  106.48     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" C5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -52.46  106.24     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 3845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 901
       0.051 -    0.102: 148
       0.102 -    0.152: 11
       0.152 -    0.203: 4
       0.203 -    0.254: 2
  Chirality restraints: 1066
  Sorted by residual:
  chirality pdb=" CA  ASN A 283 "
            pdb=" N   ASN A 283 "
            pdb=" C   ASN A 283 "
            pdb=" CB  ASN A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 283 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1063 not shown)

  Planarity restraints: 1058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 283 "    0.001 2.00e-02 2.50e+03   3.05e-02 1.16e+01
        pdb=" CG  ASN A 283 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 283 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 283 "    0.035 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 167 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   TYR B 167 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   TYR B 167 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU B 168 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 167 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   TYR A 167 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TYR A 167 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 168 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1055 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 823
        2.75 -     3.29: 6592
        3.29 -     3.82: 10801
        3.82 -     4.36: 11266
        4.36 -     4.90: 20145
  Nonbonded interactions: 49627
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   LEU A 154 "
            pdb=" OG  SER A 158 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 151 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN B  31 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.259 3.040
  ... (remaining 49622 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  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:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.410
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
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   0.033   6348  Z= 0.168
  Angle     :  0.631   8.747   8674  Z= 0.304
  Chirality :  0.039   0.254   1066
  Planarity :  0.004   0.052   1050
  Dihedral  : 16.498 106.479   2368
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.52 (0.30), residues: 780
  helix:  2.66 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.33 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  26 
 TYR   0.015   0.001   TYR B 216 
 PHE   0.020   0.001   PHE B 395 
 TRP   0.013   0.001   TRP B 414 
 HIS   0.003   0.001   HIS B  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6332)
  covalent geometry    : angle       0.59690 ( 8630)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.63626 (    8)
  hydrogen bonds       : bond        0.11116 (  562)
  hydrogen bonds       : angle       4.77758 ( 1680)
  link_BETA1-4         : bond        0.01570 (    4)
  link_BETA1-4         : angle       3.77055 (   12)
  link_NAG-ASN         : bond        0.00613 (    8)
  link_NAG-ASN         : angle       2.89512 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7340 (t0) cc_final: 0.7015 (t0)
REVERT: A  406 MET cc_start: 0.8207 (tmm) cc_final: 0.7957 (tmm)
REVERT: B  127 ASP cc_start: 0.7753 (t0) cc_final: 0.7064 (t0)
REVERT: B  166 ASP cc_start: 0.7518 (p0) cc_final: 0.7070 (m-30)
REVERT: B  210 TYR cc_start: 0.6851 (t80) cc_final: 0.6566 (t80)
REVERT: B  341 GLU cc_start: 0.8057 (pp20) cc_final: 0.7557 (pp20)
REVERT: B  406 MET cc_start: 0.8378 (tmm) cc_final: 0.8087 (tmm)
REVERT: B  412 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7477 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0626
  time to fit residues: 17.8553
Evaluate side-chains
  188 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.176506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.151278 restraints weight = 8757.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.155219 restraints weight = 5126.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.157739 restraints weight = 3533.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.159162 restraints weight = 2751.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.160289 restraints weight = 2365.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6348  Z= 0.141
  Angle     :  0.605   7.717   8674  Z= 0.296
  Chirality :  0.039   0.195   1066
  Planarity :  0.004   0.054   1050
  Dihedral  : 11.288  74.729   1090
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.23 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.60 (0.29), residues: 780
  helix:  2.71 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.35 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 192 
 TYR   0.010   0.001   TYR B 167 
 PHE   0.014   0.001   PHE A  47 
 TRP   0.008   0.001   TRP B  12 
 HIS   0.001   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6332)
  covalent geometry    : angle       0.58672 ( 8630)
  SS BOND              : bond        0.00328 (    4)
  SS BOND              : angle       1.37104 (    8)
  hydrogen bonds       : bond        0.04693 (  562)
  hydrogen bonds       : angle       4.14104 ( 1680)
  link_BETA1-4         : bond        0.01255 (    4)
  link_BETA1-4         : angle       3.40591 (   12)
  link_NAG-ASN         : bond        0.00567 (    8)
  link_NAG-ASN         : angle       1.49187 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 212
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7450 (t0) cc_final: 0.6928 (t0)
REVERT: A  406 MET cc_start: 0.8236 (tmm) cc_final: 0.8030 (tmm)
REVERT: B  127 ASP cc_start: 0.7838 (t0) cc_final: 0.7151 (t0)
REVERT: B  166 ASP cc_start: 0.7629 (p0) cc_final: 0.6862 (m-30)
REVERT: B  210 TYR cc_start: 0.6830 (t80) cc_final: 0.6413 (t80)
REVERT: B  325 GLN cc_start: 0.7454 (mp10) cc_final: 0.7188 (mp10)
REVERT: B  341 GLU cc_start: 0.7989 (pp20) cc_final: 0.7461 (pp20)
REVERT: B  406 MET cc_start: 0.8500 (tmm) cc_final: 0.8217 (tmm)
REVERT: B  412 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7267 (ttm170)
  outliers start: 12
  outliers final: 9
  residues processed: 214
  average time/residue: 0.0588
  time to fit residues: 17.6346
Evaluate side-chains
  207 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 198
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.0010
   chunk 59 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0070
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5204

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.179012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.154291 restraints weight = 8691.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.157851 restraints weight = 5206.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.160043 restraints weight = 3693.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.161696 restraints weight = 2963.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.162501 restraints weight = 2549.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6348  Z= 0.129
  Angle     :  0.609   8.824   8674  Z= 0.288
  Chirality :  0.038   0.181   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  8.500  55.776   1090
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.36 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.64 (0.29), residues: 780
  helix:  2.76 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.21 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 295 
 TYR   0.008   0.001   TYR B 167 
 PHE   0.019   0.001   PHE A  47 
 TRP   0.007   0.001   TRP A  13 
 HIS   0.001   0.000   HIS B  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6332)
  covalent geometry    : angle       0.58872 ( 8630)
  SS BOND              : bond        0.00393 (    4)
  SS BOND              : angle       1.54387 (    8)
  hydrogen bonds       : bond        0.04311 (  562)
  hydrogen bonds       : angle       3.99666 ( 1680)
  link_BETA1-4         : bond        0.01356 (    4)
  link_BETA1-4         : angle       3.62541 (   12)
  link_NAG-ASN         : bond        0.00579 (    8)
  link_NAG-ASN         : angle       1.35894 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 219
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7382 (t0) cc_final: 0.6716 (t0)
REVERT: A  209 GLU cc_start: 0.7682 (tp30) cc_final: 0.7464 (tp30)
REVERT: A  412 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7194 (ttm170)
REVERT: B  127 ASP cc_start: 0.7770 (t0) cc_final: 0.7081 (t0)
REVERT: B  166 ASP cc_start: 0.7730 (p0) cc_final: 0.7373 (p0)
REVERT: B  210 TYR cc_start: 0.6765 (t80) cc_final: 0.6499 (t80)
REVERT: B  325 GLN cc_start: 0.7497 (mp10) cc_final: 0.7266 (mp10)
REVERT: B  341 GLU cc_start: 0.7905 (pp20) cc_final: 0.7449 (pp20)
REVERT: B  406 MET cc_start: 0.8541 (tmm) cc_final: 0.8263 (tmm)
REVERT: B  412 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7282 (ttm170)
  outliers start: 14
  outliers final: 11
  residues processed: 221
  average time/residue: 0.0567
  time to fit residues: 17.5934
Evaluate side-chains
  218 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 207
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0370
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.175295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.149723 restraints weight = 8782.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.153699 restraints weight = 5048.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.156313 restraints weight = 3460.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.157930 restraints weight = 2681.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.158462 restraints weight = 2275.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6348  Z= 0.137
  Angle     :  0.611   8.068   8674  Z= 0.292
  Chirality :  0.039   0.253   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  6.644  53.666   1090
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.10 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.69 (0.29), residues: 780
  helix:  2.82 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.02 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  26 
 TYR   0.007   0.001   TYR A 374 
 PHE   0.018   0.001   PHE B 173 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6332)
  covalent geometry    : angle       0.58583 ( 8630)
  SS BOND              : bond        0.00691 (    4)
  SS BOND              : angle       1.86211 (    8)
  hydrogen bonds       : bond        0.04186 (  562)
  hydrogen bonds       : angle       3.88687 ( 1680)
  link_BETA1-4         : bond        0.01544 (    4)
  link_BETA1-4         : angle       4.03900 (   12)
  link_NAG-ASN         : bond        0.00559 (    8)
  link_NAG-ASN         : angle       1.42699 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 219
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7387 (t0) cc_final: 0.6601 (t0)
REVERT: A  412 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7220 (ttm170)
REVERT: B  127 ASP cc_start: 0.7754 (t0) cc_final: 0.7071 (t0)
REVERT: B  166 ASP cc_start: 0.8037 (p0) cc_final: 0.6824 (p0)
REVERT: B  210 TYR cc_start: 0.6893 (t80) cc_final: 0.6564 (t80)
REVERT: B  341 GLU cc_start: 0.7926 (pp20) cc_final: 0.7465 (pp20)
REVERT: B  406 MET cc_start: 0.8655 (tmm) cc_final: 0.8317 (tmm)
REVERT: B  412 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7127 (ttm170)
  outliers start: 11
  outliers final: 10
  residues processed: 221
  average time/residue: 0.0612
  time to fit residues: 18.7732
Evaluate side-chains
  219 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 209
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0060
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.5396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.177740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.152889 restraints weight = 8806.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.156685 restraints weight = 5166.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159175 restraints weight = 3577.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.160638 restraints weight = 2805.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.161440 restraints weight = 2412.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6348  Z= 0.128
  Angle     :  0.605   8.535   8674  Z= 0.288
  Chirality :  0.038   0.244   1066
  Planarity :  0.004   0.058   1050
  Dihedral  :  5.890  46.304   1090
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 22.94 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.78 (0.29), residues: 780
  helix:  2.89 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.07 (0.57), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 164 
 TYR   0.010   0.001   TYR B 374 
 PHE   0.020   0.001   PHE B 173 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6332)
  covalent geometry    : angle       0.57843 ( 8630)
  SS BOND              : bond        0.00416 (    4)
  SS BOND              : angle       1.67043 (    8)
  hydrogen bonds       : bond        0.04018 (  562)
  hydrogen bonds       : angle       3.81847 ( 1680)
  link_BETA1-4         : bond        0.01588 (    4)
  link_BETA1-4         : angle       4.31269 (   12)
  link_NAG-ASN         : bond        0.00571 (    8)
  link_NAG-ASN         : angle       1.39242 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7545 (t0) cc_final: 0.6880 (t70)
REVERT: A  166 ASP cc_start: 0.8044 (p0) cc_final: 0.7570 (p0)
REVERT: A  412 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7230 (ttm170)
REVERT: B  166 ASP cc_start: 0.7941 (p0) cc_final: 0.7354 (p0)
REVERT: B  169 GLN cc_start: 0.6689 (mp10) cc_final: 0.6373 (mp10)
REVERT: B  210 TYR cc_start: 0.6868 (t80) cc_final: 0.6530 (t80)
REVERT: B  325 GLN cc_start: 0.7788 (mp10) cc_final: 0.7101 (mp10)
REVERT: B  337 PHE cc_start: 0.6797 (m-10) cc_final: 0.6554 (m-10)
REVERT: B  341 GLU cc_start: 0.7985 (pp20) cc_final: 0.7578 (pp20)
REVERT: B  406 MET cc_start: 0.8673 (tmm) cc_final: 0.8327 (tmm)
  outliers start: 10
  outliers final: 9
  residues processed: 217
  average time/residue: 0.0590
  time to fit residues: 17.9456
Evaluate side-chains
  220 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 211
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.176344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.151280 restraints weight = 8721.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.155134 restraints weight = 5083.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.157687 restraints weight = 3499.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.159090 restraints weight = 2734.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.160208 restraints weight = 2352.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6348  Z= 0.137
  Angle     :  0.617   8.623   8674  Z= 0.294
  Chirality :  0.039   0.243   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.619  41.490   1090
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.55 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.82 (0.29), residues: 780
  helix:  2.91 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop : -0.03 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 164 
 TYR   0.007   0.001   TYR B   8 
 PHE   0.018   0.001   PHE A  47 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6332)
  covalent geometry    : angle       0.59181 ( 8630)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       1.76245 (    8)
  hydrogen bonds       : bond        0.04055 (  562)
  hydrogen bonds       : angle       3.80799 ( 1680)
  link_BETA1-4         : bond        0.01471 (    4)
  link_BETA1-4         : angle       4.20196 (   12)
  link_NAG-ASN         : bond        0.00562 (    8)
  link_NAG-ASN         : angle       1.33392 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7523 (t0) cc_final: 0.6858 (t70)
REVERT: A  166 ASP cc_start: 0.7970 (p0) cc_final: 0.7540 (p0)
REVERT: A  412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7134 (ttm170)
REVERT: B  166 ASP cc_start: 0.7734 (p0) cc_final: 0.7318 (p0)
REVERT: B  210 TYR cc_start: 0.6967 (t80) cc_final: 0.6658 (t80)
REVERT: B  325 GLN cc_start: 0.7786 (mp10) cc_final: 0.7153 (mp10)
REVERT: B  337 PHE cc_start: 0.6778 (m-10) cc_final: 0.6532 (m-10)
REVERT: B  341 GLU cc_start: 0.7770 (pp20) cc_final: 0.7430 (pp20)
REVERT: B  366 ASP cc_start: 0.8896 (t0) cc_final: 0.8670 (t70)
REVERT: B  406 MET cc_start: 0.8622 (tmm) cc_final: 0.8263 (tmm)
  outliers start: 15
  outliers final: 14
  residues processed: 219
  average time/residue: 0.0580
  time to fit residues: 17.8623
Evaluate side-chains
  226 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 212
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0570
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.176038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.151561 restraints weight = 8757.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.155228 restraints weight = 5168.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.157438 restraints weight = 3604.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.159204 restraints weight = 2871.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.160023 restraints weight = 2433.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6348  Z= 0.134
  Angle     :  0.621   8.268   8674  Z= 0.295
  Chirality :  0.038   0.239   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.414  38.924   1090
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 25.23 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.92 (0.29), residues: 780
  helix:  2.96 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.07 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 164 
 TYR   0.008   0.001   TYR A 374 
 PHE   0.019   0.001   PHE B  47 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6332)
  covalent geometry    : angle       0.59581 ( 8630)
  SS BOND              : bond        0.00470 (    4)
  SS BOND              : angle       1.81059 (    8)
  hydrogen bonds       : bond        0.04043 (  562)
  hydrogen bonds       : angle       3.78150 ( 1680)
  link_BETA1-4         : bond        0.01472 (    4)
  link_BETA1-4         : angle       4.17475 (   12)
  link_NAG-ASN         : bond        0.00560 (    8)
  link_NAG-ASN         : angle       1.33748 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7503 (t0) cc_final: 0.6835 (t70)
REVERT: A  166 ASP cc_start: 0.7925 (p0) cc_final: 0.7478 (p0)
REVERT: A  412 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7142 (ttm170)
REVERT: B  166 ASP cc_start: 0.7744 (p0) cc_final: 0.7324 (p0)
REVERT: B  210 TYR cc_start: 0.6801 (t80) cc_final: 0.6516 (t80)
REVERT: B  325 GLN cc_start: 0.7764 (mp10) cc_final: 0.7227 (mp10)
REVERT: B  337 PHE cc_start: 0.6676 (m-10) cc_final: 0.6461 (m-10)
REVERT: B  341 GLU cc_start: 0.7692 (pp20) cc_final: 0.7342 (pp20)
REVERT: B  366 ASP cc_start: 0.8954 (t0) cc_final: 0.8730 (t70)
  outliers start: 13
  outliers final: 12
  residues processed: 224
  average time/residue: 0.0580
  time to fit residues: 18.3221
Evaluate side-chains
  227 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 215
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.173781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.149083 restraints weight = 8829.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.152819 restraints weight = 5174.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.155068 restraints weight = 3597.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.156881 restraints weight = 2850.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.157562 restraints weight = 2415.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6348  Z= 0.162
  Angle     :  0.661   8.281   8674  Z= 0.314
  Chirality :  0.039   0.248   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.340  39.433   1090
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.15 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.82 (0.29), residues: 780
  helix:  2.87 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.25 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 295 
 TYR   0.010   0.001   TYR B 167 
 PHE   0.017   0.001   PHE B  47 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.002   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6332)
  covalent geometry    : angle       0.63638 ( 8630)
  SS BOND              : bond        0.00555 (    4)
  SS BOND              : angle       2.10412 (    8)
  hydrogen bonds       : bond        0.04203 (  562)
  hydrogen bonds       : angle       3.84451 ( 1680)
  link_BETA1-4         : bond        0.01388 (    4)
  link_BETA1-4         : angle       4.19991 (   12)
  link_NAG-ASN         : bond        0.00508 (    8)
  link_NAG-ASN         : angle       1.39465 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 220
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7498 (t0) cc_final: 0.6829 (t70)
REVERT: A  166 ASP cc_start: 0.7899 (p0) cc_final: 0.6851 (p0)
REVERT: A  167 TYR cc_start: 0.7887 (m-10) cc_final: 0.7498 (m-10)
REVERT: A  412 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7159 (ttm170)
REVERT: B  166 ASP cc_start: 0.7768 (p0) cc_final: 0.7447 (p0)
REVERT: B  210 TYR cc_start: 0.6731 (t80) cc_final: 0.6510 (t80)
REVERT: B  337 PHE cc_start: 0.6681 (m-10) cc_final: 0.6474 (m-10)
REVERT: B  341 GLU cc_start: 0.7714 (pp20) cc_final: 0.7338 (pp20)
REVERT: B  351 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8213 (mt)
REVERT: B  366 ASP cc_start: 0.9019 (t0) cc_final: 0.8802 (t70)
  outliers start: 17
  outliers final: 15
  residues processed: 226
  average time/residue: 0.0631
  time to fit residues: 20.0645
Evaluate side-chains
  231 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.176415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.151799 restraints weight = 8749.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.155484 restraints weight = 5080.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.158095 restraints weight = 3534.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.159543 restraints weight = 2748.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.160666 restraints weight = 2357.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6348  Z= 0.131
  Angle     :  0.636   8.197   8674  Z= 0.300
  Chirality :  0.038   0.236   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.194  38.660   1090
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 26.45 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.92 (0.29), residues: 780
  helix:  2.95 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.19 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 295 
 TYR   0.008   0.001   TYR B 167 
 PHE   0.020   0.001   PHE A  47 
 TRP   0.012   0.001   TRP A 257 
 HIS   0.001   0.000   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6332)
  covalent geometry    : angle       0.61273 ( 8630)
  SS BOND              : bond        0.00476 (    4)
  SS BOND              : angle       1.79240 (    8)
  hydrogen bonds       : bond        0.04042 (  562)
  hydrogen bonds       : angle       3.78424 ( 1680)
  link_BETA1-4         : bond        0.01427 (    4)
  link_BETA1-4         : angle       4.10507 (   12)
  link_NAG-ASN         : bond        0.00577 (    8)
  link_NAG-ASN         : angle       1.37578 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 223
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7465 (t0) cc_final: 0.6835 (t70)
REVERT: A  166 ASP cc_start: 0.7854 (p0) cc_final: 0.7265 (p0)
REVERT: A  412 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7219 (ttm170)
REVERT: B  166 ASP cc_start: 0.7698 (p0) cc_final: 0.6620 (p0)
REVERT: B  210 TYR cc_start: 0.6802 (t80) cc_final: 0.6521 (t80)
REVERT: B  337 PHE cc_start: 0.6545 (m-10) cc_final: 0.6311 (m-10)
REVERT: B  351 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8068 (mt)
  outliers start: 14
  outliers final: 13
  residues processed: 228
  average time/residue: 0.0653
  time to fit residues: 21.0257
Evaluate side-chains
  233 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 219
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.174707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.149938 restraints weight = 8797.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.153829 restraints weight = 5074.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.156446 restraints weight = 3478.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.157904 restraints weight = 2693.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159049 restraints weight = 2305.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6348  Z= 0.144
  Angle     :  0.660   8.446   8674  Z= 0.314
  Chirality :  0.039   0.239   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.171  39.673   1090
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.84 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.90 (0.29), residues: 780
  helix:  2.92 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.26 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 164 
 TYR   0.010   0.001   TYR B 167 
 PHE   0.019   0.001   PHE A  47 
 TRP   0.014   0.001   TRP B 257 
 HIS   0.001   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6332)
  covalent geometry    : angle       0.63643 ( 8630)
  SS BOND              : bond        0.00512 (    4)
  SS BOND              : angle       2.00576 (    8)
  hydrogen bonds       : bond        0.04104 (  562)
  hydrogen bonds       : angle       3.82343 ( 1680)
  link_BETA1-4         : bond        0.01382 (    4)
  link_BETA1-4         : angle       4.11934 (   12)
  link_NAG-ASN         : bond        0.00547 (    8)
  link_NAG-ASN         : angle       1.37549 (   24)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7542 (t0) cc_final: 0.6853 (t70)
REVERT: A  166 ASP cc_start: 0.7863 (p0) cc_final: 0.7163 (p0)
REVERT: A  412 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7214 (ttm170)
REVERT: B  166 ASP cc_start: 0.7680 (p0) cc_final: 0.7420 (p0)
REVERT: B  210 TYR cc_start: 0.6884 (t80) cc_final: 0.6610 (t80)
REVERT: B  337 PHE cc_start: 0.6589 (m-10) cc_final: 0.6348 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 226
  average time/residue: 0.0587
  time to fit residues: 18.8822
Evaluate side-chains
  229 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 214
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 348 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.174738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.149898 restraints weight = 8744.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.153819 restraints weight = 5086.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.156118 restraints weight = 3499.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.157933 restraints weight = 2750.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.158626 restraints weight = 2326.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6348  Z= 0.147
  Angle     :  0.653   8.591   8674  Z= 0.311
  Chirality :  0.039   0.243   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.159  40.147   1090
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.15 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.85 (0.29), residues: 780
  helix:  2.88 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.29 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 164 
 TYR   0.009   0.001   TYR B 167 
 PHE   0.018   0.001   PHE A  47 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.002   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6332)
  covalent geometry    : angle       0.62980 ( 8630)
  SS BOND              : bond        0.00523 (    4)
  SS BOND              : angle       2.08448 (    8)
  hydrogen bonds       : bond        0.04131 (  562)
  hydrogen bonds       : angle       3.84258 ( 1680)
  link_BETA1-4         : bond        0.01376 (    4)
  link_BETA1-4         : angle       4.07707 (   12)
  link_NAG-ASN         : bond        0.00544 (    8)
  link_NAG-ASN         : angle       1.37841 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1053.94 seconds
wall clock time: 18 minutes 52.60 seconds (1132.60 seconds total)