Starting phenix.real_space_refine
on Thu Jul  2 03:09:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7p5m_13201/07_2026/7p5m_13201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5m_13201/07_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_13201/07_2026/7p5m_13201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2026/7p5m_13201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2026/7p5m_13201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2026/7p5m_13201.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_2026/7p5m_13201.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7p5m_13201/07_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-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 2
  Time building chain proxies: 1.62, per 1000 atoms: 0.26
  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: 0.59
  Conformation dependent library (CDL) restraints added in 370.3 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: 0.14
  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: 0.94

  Time building geometry restraints manager: 0.78 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 -    16.05: 3193
       16.05 -    32.10: 300
       32.10 -    48.15: 91
       48.15 -    64.20: 6
       64.20 -    80.25: 6
  Dihedral angle restraints: 3596
    sinusoidal: 1310
      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=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.60   30.40     1      1.00e+01 1.00e-02 1.32e+01
  dihedral pdb=" CA  ASN B 283 "
           pdb=" C   ASN B 283 "
           pdb=" N   VAL B 284 "
           pdb=" CA  VAL B 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 3593 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.470
  Find NCS groups from input model:        0.110
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
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  : 13.681  80.248   2116
  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/Z
  covalent geometry    : bond        0.00344 /  0.17 ( 6332)
  covalent geometry    : angle       0.59690 /  0.30 ( 8630)
  SS BOND              : bond        0.00295 /  0.14 (    4)
  SS BOND              : angle       0.63626 /  0.36 (    8)
  hydrogen bonds       : bond        0.11116 /  7.44 (  562)
  hydrogen bonds       : angle       4.77758 /  3.40 ( 1680)
  link_BETA1-4         : bond        0.01570 /  0.71 (    4)
  link_BETA1-4         : angle       3.77055 /  2.15 (   12)
  link_NAG-ASN         : bond        0.00613 /  0.35 (    8)
  link_NAG-ASN         : angle       2.89512 /  1.54 (   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  : 0.220 
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: 0.0652
  time to fit residues: 18.7231
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  : 0.264 
-------------------------------------------------------------------------------
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...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.177820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152780 restraints weight = 8836.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.156475 restraints weight = 5310.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.158576 restraints weight = 3739.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.160324 restraints weight = 3000.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.161152 restraints weight = 2571.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6348  Z= 0.139
  Angle     :  0.589   7.645   8674  Z= 0.293
  Chirality :  0.038   0.168   1066
  Planarity :  0.004   0.053   1050
  Dihedral  :  3.762  20.142    838
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.93 %
    Favored  : 86.24 %
  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:  3.57 (0.29), residues: 780
  helix:  2.69 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop :  0.30 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  26 
 TYR   0.011   0.001   TYR B 167 
 PHE   0.013   0.001   PHE A  47 
 TRP   0.007   0.001   TRP B  12 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.14 ( 6332)
  covalent geometry    : angle       0.56864 /  0.29 ( 8630)
  SS BOND              : bond        0.00788 /  0.36 (    4)
  SS BOND              : angle       1.89775 /  1.03 (    8)
  hydrogen bonds       : bond        0.04725 /  3.16 (  562)
  hydrogen bonds       : angle       4.15192 /  2.97 ( 1680)
  link_BETA1-4         : bond        0.01399 /  0.64 (    4)
  link_BETA1-4         : angle       3.39264 /  1.94 (   12)
  link_NAG-ASN         : bond        0.00566 /  0.28 (    8)
  link_NAG-ASN         : angle       1.41367 /  0.93 (   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
  223 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 211
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7352 (t0) cc_final: 0.6868 (t0)
REVERT: B  127 ASP cc_start: 0.7773 (t0) cc_final: 0.7125 (t0)
REVERT: B  166 ASP cc_start: 0.7547 (p0) cc_final: 0.6794 (m-30)
REVERT: B  210 TYR cc_start: 0.6764 (t80) cc_final: 0.6351 (t80)
REVERT: B  325 GLN cc_start: 0.7392 (mp10) cc_final: 0.7141 (mp10)
REVERT: B  341 GLU cc_start: 0.7902 (pp20) cc_final: 0.7418 (pp20)
REVERT: B  406 MET cc_start: 0.8472 (tmm) cc_final: 0.8218 (tmm)
REVERT: B  412 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7282 (ttm170)
  outliers start: 12
  outliers final: 9
  residues processed: 213
  average time/residue: 0.0606
  time to fit residues: 18.2064
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  : 0.215 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 70 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.176217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.150625 restraints weight = 8705.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154499 restraints weight = 5042.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.157103 restraints weight = 3481.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.158796 restraints weight = 2714.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.159685 restraints weight = 2303.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1416

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= 0.146
  Angle     :  0.593   8.098   8674  Z= 0.290
  Chirality :  0.038   0.177   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.777  18.212    838
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.28 %
    Favored  : 80.43 %
  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:  3.59 (0.29), residues: 780
  helix:  2.72 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.25 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 295 
 TYR   0.007   0.001   TYR B 374 
 PHE   0.021   0.001   PHE A  47 
 TRP   0.007   0.001   TRP B 414 
 HIS   0.002   0.001   HIS A 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 6332)
  covalent geometry    : angle       0.57412 /  0.29 ( 8630)
  SS BOND              : bond        0.00403 /  0.18 (    4)
  SS BOND              : angle       1.77660 /  0.97 (    8)
  hydrogen bonds       : bond        0.04413 /  2.94 (  562)
  hydrogen bonds       : angle       4.01801 /  2.88 ( 1680)
  link_BETA1-4         : bond        0.01359 /  0.62 (    4)
  link_BETA1-4         : angle       3.37568 /  1.93 (   12)
  link_NAG-ASN         : bond        0.00555 /  0.26 (    8)
  link_NAG-ASN         : angle       1.32028 /  0.88 (   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
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7330 (t0) cc_final: 0.6683 (t0)
REVERT: A  209 GLU cc_start: 0.7724 (tp30) cc_final: 0.7502 (tp30)
REVERT: A  412 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7207 (ttm170)
REVERT: B  127 ASP cc_start: 0.7741 (t0) cc_final: 0.7094 (t0)
REVERT: B  166 ASP cc_start: 0.7696 (p0) cc_final: 0.7356 (p0)
REVERT: B  210 TYR cc_start: 0.6751 (t80) cc_final: 0.6489 (t80)
REVERT: B  325 GLN cc_start: 0.7482 (mp10) cc_final: 0.7271 (mp10)
REVERT: B  341 GLU cc_start: 0.7796 (pp20) cc_final: 0.7379 (pp20)
REVERT: B  406 MET cc_start: 0.8530 (tmm) cc_final: 0.8280 (tmm)
REVERT: B  412 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7279 (ttm170)
  outliers start: 15
  outliers final: 12
  residues processed: 222
  average time/residue: 0.0591
  time to fit residues: 18.4798
Evaluate side-chains
  217 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 205
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
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   54 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0570
   chunk 55 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0770
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.5256

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.176869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.151697 restraints weight = 8780.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.155490 restraints weight = 5142.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.157984 restraints weight = 3575.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.159679 restraints weight = 2805.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.160537 restraints weight = 2387.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6348  Z= 0.132
  Angle     :  0.593   8.124   8674  Z= 0.288
  Chirality :  0.038   0.259   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.703  16.890    838
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.56 %
    Favored  : 76.61 %
  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:  3.68 (0.29), residues: 780
  helix:  2.81 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.03 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 295 
 TYR   0.008   0.001   TYR A 374 
 PHE   0.021   0.001   PHE B 173 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 6332)
  covalent geometry    : angle       0.57434 /  0.28 ( 8630)
  SS BOND              : bond        0.00315 /  0.14 (    4)
  SS BOND              : angle       1.72258 /  0.92 (    8)
  hydrogen bonds       : bond        0.04198 /  2.78 (  562)
  hydrogen bonds       : angle       3.91876 /  2.80 ( 1680)
  link_BETA1-4         : bond        0.01385 /  0.63 (    4)
  link_BETA1-4         : angle       3.34373 /  1.91 (   12)
  link_NAG-ASN         : bond        0.00533 /  0.23 (    8)
  link_NAG-ASN         : angle       1.39392 /  0.92 (   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
  232 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 220
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7487 (t0) cc_final: 0.6660 (t0)
REVERT: A  412 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7214 (ttm170)
REVERT: B  127 ASP cc_start: 0.7816 (t0) cc_final: 0.7105 (t0)
REVERT: B  166 ASP cc_start: 0.8237 (p0) cc_final: 0.7055 (p0)
REVERT: B  210 TYR cc_start: 0.6862 (t80) cc_final: 0.6484 (t80)
REVERT: B  325 GLN cc_start: 0.7514 (mp10) cc_final: 0.7243 (mp10)
REVERT: B  341 GLU cc_start: 0.8034 (pp20) cc_final: 0.7510 (pp20)
REVERT: B  406 MET cc_start: 0.8672 (tmm) cc_final: 0.8310 (tmm)
REVERT: B  412 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7159 (ttm170)
  outliers start: 12
  outliers final: 10
  residues processed: 222
  average time/residue: 0.0632
  time to fit residues: 19.5322
Evaluate side-chains
  221 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 211
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.1980
   chunk 3 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.151282 restraints weight = 8770.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.155178 restraints weight = 5255.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157672 restraints weight = 3651.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159364 restraints weight = 2846.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.160242 restraints weight = 2406.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6348  Z= 0.128
  Angle     :  0.589   7.532   8674  Z= 0.285
  Chirality :  0.037   0.244   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.677  16.031    838
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 22.94 %
    Favored  : 75.69 %
  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:  3.73 (0.29), residues: 780
  helix:  2.86 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.09 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 164 
 TYR   0.008   0.001   TYR B 374 
 PHE   0.023   0.002   PHE B 173 
 TRP   0.010   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  18 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.13 ( 6332)
  covalent geometry    : angle       0.57035 /  0.28 ( 8630)
  SS BOND              : bond        0.00751 /  0.35 (    4)
  SS BOND              : angle       1.61642 /  0.86 (    8)
  hydrogen bonds       : bond        0.04079 /  2.70 (  562)
  hydrogen bonds       : angle       3.84281 /  2.75 ( 1680)
  link_BETA1-4         : bond        0.01337 /  0.61 (    4)
  link_BETA1-4         : angle       3.36148 /  1.92 (   12)
  link_NAG-ASN         : bond        0.00531 /  0.25 (    8)
  link_NAG-ASN         : angle       1.41424 /  0.93 (   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
  223 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 214
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7613 (t0) cc_final: 0.6919 (t70)
REVERT: A  166 ASP cc_start: 0.8129 (p0) cc_final: 0.7623 (p0)
REVERT: A  412 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7234 (ttm170)
REVERT: B  166 ASP cc_start: 0.8029 (p0) cc_final: 0.7736 (p0)
REVERT: B  210 TYR cc_start: 0.6883 (t80) cc_final: 0.6549 (t80)
REVERT: B  337 PHE cc_start: 0.6883 (m-10) cc_final: 0.6604 (m-10)
REVERT: B  341 GLU cc_start: 0.8042 (pp20) cc_final: 0.7597 (pp20)
REVERT: B  406 MET cc_start: 0.8678 (tmm) cc_final: 0.8328 (tmm)
  outliers start: 9
  outliers final: 8
  residues processed: 216
  average time/residue: 0.0588
  time to fit residues: 17.8931
Evaluate side-chains
  219 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 211
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  226 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:    0.9980
   chunk 65 optimal weight:    0.0980
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.177145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.152139 restraints weight = 8740.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.155784 restraints weight = 5228.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.158148 restraints weight = 3678.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.159752 restraints weight = 2916.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.160581 restraints weight = 2503.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1962

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= 0.132
  Angle     :  0.603   9.191   8674  Z= 0.290
  Chirality :  0.038   0.236   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.630  14.684    838
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.63 %
    Favored  : 74.92 %
  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 : -0.04 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 164 
 TYR   0.009   0.001   TYR B 374 
 PHE   0.023   0.002   PHE B 173 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 ( 6332)
  covalent geometry    : angle       0.58473 /  0.29 ( 8630)
  SS BOND              : bond        0.00593 /  0.28 (    4)
  SS BOND              : angle       1.82066 /  0.97 (    8)
  hydrogen bonds       : bond        0.04059 /  2.69 (  562)
  hydrogen bonds       : angle       3.81163 /  2.73 ( 1680)
  link_BETA1-4         : bond        0.01306 /  0.60 (    4)
  link_BETA1-4         : angle       3.33299 /  1.90 (   12)
  link_NAG-ASN         : bond        0.00497 /  0.22 (    8)
  link_NAG-ASN         : angle       1.36016 /  0.90 (   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: 16
    poor density    : 214
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7532 (t0) cc_final: 0.6864 (t70)
REVERT: A  166 ASP cc_start: 0.7971 (p0) cc_final: 0.7517 (p0)
REVERT: A  412 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7202 (ttm170)
REVERT: B  166 ASP cc_start: 0.7890 (p0) cc_final: 0.7548 (p0)
REVERT: B  209 GLU cc_start: 0.7647 (tp30) cc_final: 0.7443 (tp30)
REVERT: B  210 TYR cc_start: 0.6889 (t80) cc_final: 0.6579 (t80)
REVERT: B  325 GLN cc_start: 0.7729 (mp10) cc_final: 0.7106 (mp10)
REVERT: B  337 PHE cc_start: 0.6794 (m-10) cc_final: 0.6562 (m-10)
REVERT: B  341 GLU cc_start: 0.7890 (pp20) cc_final: 0.7522 (pp20)
REVERT: B  406 MET cc_start: 0.8621 (tmm) cc_final: 0.8263 (tmm)
  outliers start: 16
  outliers final: 16
  residues processed: 218
  average time/residue: 0.0582
  time to fit residues: 17.7456
Evaluate side-chains
  225 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 209
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
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   56 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
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  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:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.175828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.151030 restraints weight = 8757.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154533 restraints weight = 5245.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.156922 restraints weight = 3698.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.158516 restraints weight = 2935.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.159170 restraints weight = 2516.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6348  Z= 0.142
  Angle     :  0.616   8.099   8674  Z= 0.296
  Chirality :  0.038   0.234   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.618  14.481    838
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.01 %
    Favored  : 73.39 %
  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:  3.84 (0.29), residues: 780
  helix:  2.91 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.04 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 164 
 TYR   0.010   0.001   TYR B 374 
 PHE   0.021   0.001   PHE A  47 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 6332)
  covalent geometry    : angle       0.59757 /  0.29 ( 8630)
  SS BOND              : bond        0.00527 /  0.25 (    4)
  SS BOND              : angle       1.94864 /  1.04 (    8)
  hydrogen bonds       : bond        0.04076 /  2.71 (  562)
  hydrogen bonds       : angle       3.80596 /  2.72 ( 1680)
  link_BETA1-4         : bond        0.01297 /  0.59 (    4)
  link_BETA1-4         : angle       3.37435 /  1.92 (   12)
  link_NAG-ASN         : bond        0.00492 /  0.22 (    8)
  link_NAG-ASN         : angle       1.40156 /  0.93 (   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
  234 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 217
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7485 (t0) cc_final: 0.6829 (t70)
REVERT: A  166 ASP cc_start: 0.7907 (p0) cc_final: 0.7462 (p0)
REVERT: A  412 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7121 (ttm170)
REVERT: B  166 ASP cc_start: 0.7776 (p0) cc_final: 0.7435 (p0)
REVERT: B  209 GLU cc_start: 0.7703 (tp30) cc_final: 0.7500 (tp30)
REVERT: B  210 TYR cc_start: 0.6828 (t80) cc_final: 0.6474 (t80)
REVERT: B  325 GLN cc_start: 0.7729 (mp10) cc_final: 0.7133 (mp10)
REVERT: B  337 PHE cc_start: 0.6701 (m-10) cc_final: 0.6477 (m-10)
REVERT: B  341 GLU cc_start: 0.7747 (pp20) cc_final: 0.7395 (pp20)
REVERT: B  366 ASP cc_start: 0.8820 (t70) cc_final: 0.8614 (t70)
REVERT: B  406 MET cc_start: 0.8607 (tmm) cc_final: 0.8275 (tmm)
  outliers start: 17
  outliers final: 16
  residues processed: 222
  average time/residue: 0.0592
  time to fit residues: 18.5557
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  : 0.218 
-------------------------------------------------------------------------------
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  226 ILE
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   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.8182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.176042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.150836 restraints weight = 8838.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.154680 restraints weight = 5113.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157328 restraints weight = 3529.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.158798 restraints weight = 2736.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.159956 restraints weight = 2343.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6348  Z= 0.141
  Angle     :  0.632   8.053   8674  Z= 0.302
  Chirality :  0.038   0.230   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.647  14.244    838
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.77 %
    Favored  : 72.17 %
  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:  3.84 (0.29), residues: 780
  helix:  2.89 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.15 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 164 
 TYR   0.007   0.001   TYR B 374 
 PHE   0.024   0.002   PHE B 173 
 TRP   0.012   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 6332)
  covalent geometry    : angle       0.61317 /  0.30 ( 8630)
  SS BOND              : bond        0.00520 /  0.25 (    4)
  SS BOND              : angle       1.96508 /  1.04 (    8)
  hydrogen bonds       : bond        0.04070 /  2.71 (  562)
  hydrogen bonds       : angle       3.81238 /  2.72 ( 1680)
  link_BETA1-4         : bond        0.01281 /  0.59 (    4)
  link_BETA1-4         : angle       3.37607 /  1.92 (   12)
  link_NAG-ASN         : bond        0.00485 /  0.22 (    8)
  link_NAG-ASN         : angle       1.40523 /  0.92 (   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
  241 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 221
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7512 (t0) cc_final: 0.6845 (t70)
REVERT: A  166 ASP cc_start: 0.7891 (p0) cc_final: 0.7352 (p0)
REVERT: A  412 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7132 (ttm170)
REVERT: B  166 ASP cc_start: 0.7720 (p0) cc_final: 0.7406 (p0)
REVERT: B  210 TYR cc_start: 0.6856 (t80) cc_final: 0.6508 (t80)
REVERT: B  325 GLN cc_start: 0.7764 (mp10) cc_final: 0.7195 (mp10)
REVERT: B  337 PHE cc_start: 0.6688 (m-10) cc_final: 0.6431 (m-10)
REVERT: B  341 GLU cc_start: 0.7716 (pp20) cc_final: 0.7403 (pp20)
REVERT: B  366 ASP cc_start: 0.8941 (t70) cc_final: 0.8722 (t70)
  outliers start: 20
  outliers final: 18
  residues processed: 228
  average time/residue: 0.0567
  time to fit residues: 18.1491
Evaluate side-chains
  236 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 218
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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  245 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  226 ILE
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:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0370
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.4258

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.177438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.152978 restraints weight = 8782.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.156669 restraints weight = 5188.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.159060 restraints weight = 3621.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.160468 restraints weight = 2864.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.161576 restraints weight = 2475.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6348  Z= 0.127
  Angle     :  0.623   7.803   8674  Z= 0.297
  Chirality :  0.037   0.222   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.667  13.935    838
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.38 %
    Favored  : 72.17 %
  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 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 164 
 TYR   0.009   0.001   TYR B 374 
 PHE   0.026   0.002   PHE B 173 
 TRP   0.012   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.13 ( 6332)
  covalent geometry    : angle       0.60513 /  0.29 ( 8630)
  SS BOND              : bond        0.00435 /  0.21 (    4)
  SS BOND              : angle       1.72940 /  0.91 (    8)
  hydrogen bonds       : bond        0.03971 /  2.64 (  562)
  hydrogen bonds       : angle       3.77372 /  2.69 ( 1680)
  link_BETA1-4         : bond        0.01304 /  0.60 (    4)
  link_BETA1-4         : angle       3.33398 /  1.90 (   12)
  link_NAG-ASN         : bond        0.00513 /  0.24 (    8)
  link_NAG-ASN         : angle       1.39660 /  0.92 (   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: 16
    poor density    : 221
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7550 (t0) cc_final: 0.6858 (t70)
REVERT: A  412 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7175 (ttm170)
REVERT: B  166 ASP cc_start: 0.7928 (p0) cc_final: 0.7037 (p0)
REVERT: B  210 TYR cc_start: 0.6870 (t80) cc_final: 0.6588 (t80)
REVERT: B  325 GLN cc_start: 0.7624 (mp10) cc_final: 0.7092 (mp10)
REVERT: B  366 ASP cc_start: 0.8883 (t70) cc_final: 0.8637 (t70)
  outliers start: 16
  outliers final: 16
  residues processed: 227
  average time/residue: 0.0485
  time to fit residues: 15.5949
Evaluate side-chains
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  245 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  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:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0770
   chunk 13 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 348 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.177808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.153064 restraints weight = 8805.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.156811 restraints weight = 5203.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.159272 restraints weight = 3627.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.160719 restraints weight = 2850.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.161349 restraints weight = 2455.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2322

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= 0.133
  Angle     :  0.654   8.202   8674  Z= 0.314
  Chirality :  0.038   0.221   1066
  Planarity :  0.005   0.056   1050
  Dihedral  :  3.665  13.550    838
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.84 %
    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:  2.94 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.28 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 164 
 TYR   0.008   0.001   TYR B 167 
 PHE   0.024   0.002   PHE B 173 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 6332)
  covalent geometry    : angle       0.63713 /  0.31 ( 8630)
  SS BOND              : bond        0.00463 /  0.22 (    4)
  SS BOND              : angle       1.82057 /  0.96 (    8)
  hydrogen bonds       : bond        0.03999 /  2.66 (  562)
  hydrogen bonds       : angle       3.80480 /  2.72 ( 1680)
  link_BETA1-4         : bond        0.01282 /  0.58 (    4)
  link_BETA1-4         : angle       3.35313 /  1.91 (   12)
  link_NAG-ASN         : bond        0.00494 /  0.24 (    8)
  link_NAG-ASN         : angle       1.38342 /  0.90 (   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
  236 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 218
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7607 (t0) cc_final: 0.6897 (t70)
REVERT: A  166 ASP cc_start: 0.7952 (p0) cc_final: 0.6691 (p0)
REVERT: A  167 TYR cc_start: 0.7958 (m-10) cc_final: 0.7518 (m-10)
REVERT: A  351 LEU cc_start: 0.8406 (mp) cc_final: 0.7993 (mt)
REVERT: A  412 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7175 (ttm170)
REVERT: B  166 ASP cc_start: 0.7886 (p0) cc_final: 0.7487 (p0)
REVERT: B  210 TYR cc_start: 0.6998 (t80) cc_final: 0.6714 (t80)
REVERT: B  325 GLN cc_start: 0.7722 (mp10) cc_final: 0.7163 (mp10)
REVERT: B  351 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7922 (mt)
REVERT: B  366 ASP cc_start: 0.8901 (t70) cc_final: 0.8659 (t70)
  outliers start: 18
  outliers final: 15
  residues processed: 222
  average time/residue: 0.0603
  time to fit residues: 19.0477
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  : 0.213 
-------------------------------------------------------------------------------
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  245 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  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:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.177272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152438 restraints weight = 8767.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.156266 restraints weight = 5179.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.158723 restraints weight = 3597.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.160112 restraints weight = 2823.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.161247 restraints weight = 2441.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6348  Z= 0.140
  Angle     :  0.654   8.040   8674  Z= 0.314
  Chirality :  0.038   0.225   1066
  Planarity :  0.005   0.056   1050
  Dihedral  :  3.658  13.550    838
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.69 %
    Favored  : 71.71 %
  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:  3.91 (0.29), residues: 780
  helix:  2.92 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.32 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 164 
 TYR   0.009   0.001   TYR B 374 
 PHE   0.024   0.002   PHE B 173 
 TRP   0.014   0.001   TRP B 257 
 HIS   0.001   0.000   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 6332)
  covalent geometry    : angle       0.63667 /  0.31 ( 8630)
  SS BOND              : bond        0.00477 /  0.23 (    4)
  SS BOND              : angle       1.94238 /  1.03 (    8)
  hydrogen bonds       : bond        0.04017 /  2.68 (  562)
  hydrogen bonds       : angle       3.80722 /  2.72 ( 1680)
  link_BETA1-4         : bond        0.01276 /  0.58 (    4)
  link_BETA1-4         : angle       3.35906 /  1.91 (   12)
  link_NAG-ASN         : bond        0.00487 /  0.24 (    8)
  link_NAG-ASN         : angle       1.34958 /  0.88 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1070.53 seconds
wall clock time: 19 minutes 15.84 seconds (1155.84 seconds total)