Starting phenix.real_space_refine
on Tue Feb 11 13:58:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug8_42217/02_2025/8ug8_42217.cif"
  }
  resolution = 3.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      42      5.16       5
     C    3936      2.51       5
     N     956      2.21       5
     O     982      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5916
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2958
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 9, 'TRANS': 365}
          Chain breaks: 9
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.69, per 1000 atoms: 0.79
  Number of scatterers: 5916
  At special positions: 0
  Unit cell: (80.51, 87.15, 68.89, 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      42     16.00
     O     982      8.00
     N     956      7.00
     C    3936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 659.7 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      84.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 48
      removed outlier: 3.742A  pdb=" N   VAL A  33 " --> pdb=" O   ARG A  29 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A  48 " --> pdb=" O   CYS A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 53
    Processing helix  chain 'A' and resid 59 through 59
      No H-bonds generated for 'chain 'A' and resid 59 through 59'
    Processing helix  chain 'A' and resid 60 through 84
      removed outlier: 4.024A  pdb=" N   ALA A  64 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 3.846A  pdb=" N   ARG A 104 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 158
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 165 through 193
    Processing helix  chain 'A' and resid 246 through 265
      removed outlier: 3.728A  pdb=" N   GLU A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 311
      removed outlier: 3.825A  pdb=" N   VAL A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 351
    Processing helix  chain 'A' and resid 367 through 395
      removed outlier: 3.742A  pdb=" N   LEU A 378 " --> pdb=" O   MET A 374 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLY A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   GLN A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 427
      removed outlier: 4.117A  pdb=" N   ALA A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   HIS A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 514
      removed outlier: 3.617A  pdb=" N   LYS A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 497 " --> pdb=" O   CYS A 493 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   MET A 511 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
      Proline residue:  A 512  - end of helix
    Processing helix  chain 'A' and resid 534 through 562
      Proline residue:  A 543  - end of helix
      removed outlier: 3.519A  pdb=" N   LEU A 562 " --> pdb=" O   GLU A 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 48
      removed outlier: 3.741A  pdb=" N   VAL B  33 " --> pdb=" O   ARG B  29 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER B  48 " --> pdb=" O   CYS B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 53
    Processing helix  chain 'B' and resid 59 through 59
      No H-bonds generated for 'chain 'B' and resid 59 through 59'
    Processing helix  chain 'B' and resid 60 through 84
      removed outlier: 4.025A  pdb=" N   ALA B  64 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 128
      removed outlier: 3.846A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
      Proline residue:  B 140  - end of helix
    Processing helix  chain 'B' and resid 165 through 193
    Processing helix  chain 'B' and resid 246 through 265
      removed outlier: 3.728A  pdb=" N   GLU B 250 " --> pdb=" O   PRO B 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN B 265 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 311
      removed outlier: 3.825A  pdb=" N   VAL B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE B 308 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 351
    Processing helix  chain 'B' and resid 367 through 395
      removed outlier: 3.741A  pdb=" N   LEU B 378 " --> pdb=" O   MET B 374 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLY B 379 " --> pdb=" O   GLY B 375 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   GLN B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 383 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 427
      removed outlier: 4.117A  pdb=" N   ALA B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   HIS B 427 " --> pdb=" O   ILE B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 514
      removed outlier: 3.617A  pdb=" N   LYS B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE B 497 " --> pdb=" O   CYS B 493 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   MET B 511 " --> pdb=" O   ILE B 507 " (cutoff:3.500A)
      Proline residue:  B 512  - end of helix
    Processing helix  chain 'B' and resid 534 through 562
      Proline residue:  B 543  - end of helix
      removed outlier: 3.519A  pdb=" N   LEU B 562 " --> pdb=" O   GLU B 558 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1392 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.72 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: 1770
        1.34 -     1.46: 1560
        1.46 -     1.58: 2656
        1.58 -     1.70: 0
        1.70 -     1.81: 66
  Bond restraints: 6052
  Sorted by residual:
  bond pdb=" N   SER A 157 "
       pdb=" CA  SER A 157 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.22e-02 6.72e+03 8.02e+00
  bond pdb=" N   SER B 157 "
       pdb=" CA  SER B 157 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.58e+00
  bond pdb=" N   CYS B 131 "
       pdb=" CA  CYS B 131 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.22e-02 6.72e+03 7.23e+00
  bond pdb=" N   CYS A 131 "
       pdb=" CA  CYS A 131 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 7.06e+00
  bond pdb=" N   ILE B 135 "
       pdb=" CA  ILE B 135 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.24e-02 6.50e+03 6.85e+00
  ... (remaining 6047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 8002
        1.44 -     2.88: 184
        2.88 -     4.31: 28
        4.31 -     5.75: 8
        5.75 -     7.19: 2
  Bond angle restraints: 8224
  Sorted by residual:
  angle pdb=" CA  CYS B 131 "
        pdb=" C   CYS B 131 "
        pdb=" O   CYS B 131 "
      ideal   model   delta    sigma   weight residual
     121.16  118.00    3.16 1.12e+00 7.97e-01 7.95e+00
  angle pdb=" CA  CYS A 131 "
        pdb=" C   CYS A 131 "
        pdb=" O   CYS A 131 "
      ideal   model   delta    sigma   weight residual
     121.16  118.03    3.13 1.12e+00 7.97e-01 7.81e+00
  angle pdb=" N   ALA A 134 "
        pdb=" CA  ALA A 134 "
        pdb=" C   ALA A 134 "
      ideal   model   delta    sigma   weight residual
     113.12  109.80    3.32 1.25e+00 6.40e-01 7.08e+00
  angle pdb=" N   ALA B 134 "
        pdb=" CA  ALA B 134 "
        pdb=" C   ALA B 134 "
      ideal   model   delta    sigma   weight residual
     113.12  109.80    3.32 1.25e+00 6.40e-01 7.05e+00
  angle pdb=" O   ILE B 135 "
        pdb=" C   ILE B 135 "
        pdb=" N   LYS B 136 "
      ideal   model   delta    sigma   weight residual
     121.90  124.56   -2.66 1.01e+00 9.80e-01 6.92e+00
  ... (remaining 8219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 2958
       17.15 -    34.30: 358
       34.30 -    51.45: 108
       51.45 -    68.60: 24
       68.60 -    85.75: 8
  Dihedral angle restraints: 3456
    sinusoidal: 1286
      harmonic: 2170
  Sorted by residual:
  dihedral pdb=" CA  ILE B 540 "
           pdb=" C   ILE B 540 "
           pdb=" N   CYS B 541 "
           pdb=" CA  CYS B 541 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.24  -15.76     0      5.00e+00 4.00e-02 9.93e+00
  dihedral pdb=" CA  ILE A 540 "
           pdb=" C   ILE A 540 "
           pdb=" N   CYS A 541 "
           pdb=" CA  CYS A 541 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.25  -15.75     0      5.00e+00 4.00e-02 9.92e+00
  dihedral pdb=" CB  GLU A 250 "
           pdb=" CG  GLU A 250 "
           pdb=" CD  GLU A 250 "
           pdb=" OE1 GLU A 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.77   84.77     1      3.00e+01 1.11e-03 9.70e+00
  ... (remaining 3453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 750
       0.037 -    0.073: 197
       0.073 -    0.110: 33
       0.110 -    0.147: 6
       0.147 -    0.184: 2
  Chirality restraints: 988
  Sorted by residual:
  chirality pdb=" CA  ILE B 135 "
            pdb=" N   ILE B 135 "
            pdb=" C   ILE B 135 "
            pdb=" CB  ILE B 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.44e-01
  chirality pdb=" CA  ILE A 135 "
            pdb=" N   ILE A 135 "
            pdb=" C   ILE A 135 "
            pdb=" CB  ILE A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.38e-01
  chirality pdb=" CA  PHE A 128 "
            pdb=" N   PHE A 128 "
            pdb=" C   PHE A 128 "
            pdb=" CB  PHE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 985 not shown)

  Planarity restraints: 980
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 127 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   SER A 127 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER A 127 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 128 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 127 "   -0.009 2.00e-02 2.50e+03   1.73e-02 3.01e+00
        pdb=" C   SER B 127 "    0.030 2.00e-02 2.50e+03
        pdb=" O   SER B 127 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE B 128 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 139 "   -0.026 5.00e-02 4.00e+02   3.88e-02 2.40e+00
        pdb=" N   PRO A 140 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 140 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 140 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 977 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1465
        2.79 -     3.31: 6363
        3.31 -     3.84: 10154
        3.84 -     4.37: 11961
        4.37 -     4.90: 19905
  Nonbonded interactions: 49848
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 330 "
            pdb=" OD1 ASN A 404 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OH  TYR B 330 "
            pdb=" OD1 ASN B 404 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   VAL B 188 "
            pdb=" OG  SER B 192 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   VAL A 188 "
            pdb=" OG  SER A 192 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   VAL B 147 "
            pdb=" OG1 THR B 151 "
     model   vdw
     2.289 3.040
  ... (remaining 49843 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.390
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
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   0.035   6052  Z= 0.202
  Angle     :  0.527   7.190   8224  Z= 0.325
  Chirality :  0.035   0.184    988
  Planarity :  0.003   0.039    980
  Dihedral  : 17.040  85.753   2052
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.92 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.32), residues: 710
  helix:  1.64 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -0.34 (0.58), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 509 
 HIS   0.003   0.001   HIS B 415 
 PHE   0.009   0.001   PHE B 153 
 TYR   0.013   0.001   TYR A 124 
 ARG   0.001   0.000   ARG A 397 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ASN cc_start: 0.8477 (m110) cc_final: 0.8240 (m110)
REVERT: A  400 GLN cc_start: 0.7448 (tp40) cc_final: 0.7111 (tp40)
REVERT: A  414 GLN cc_start: 0.7631 (pp30) cc_final: 0.7378 (pp30)
REVERT: A  493 CYS cc_start: 0.7494 (m) cc_final: 0.7133 (t)
REVERT: A  558 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: B  399 LEU cc_start: 0.7416 (tp) cc_final: 0.7205 (tp)
REVERT: B  558 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7944 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1501
  time to fit residues: 45.6390
Evaluate side-chains
  168 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 67 optimal weight:    0.2980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 180 ASN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 150 GLN
B 180 ASN
B 414 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.118205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.098378 restraints weight = 15345.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.100300 restraints weight = 9930.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.102300 restraints weight = 7679.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6052  Z= 0.220
  Angle     :  0.629   9.920   8224  Z= 0.326
  Chirality :  0.038   0.120    988
  Planarity :  0.005   0.049    980
  Dihedral  :  3.393  12.812    796
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.29 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.31), residues: 710
  helix:  1.60 (0.20), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.39 (0.62), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  76 
 HIS   0.004   0.001   HIS B 415 
 PHE   0.023   0.002   PHE B  79 
 TYR   0.017   0.001   TYR A 548 
 ARG   0.003   0.000   ARG A 366 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 PRO cc_start: 0.6846 (Cg_exo) cc_final: 0.6414 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5229 (mmt-90) cc_final: 0.3825 (mtt90)
REVERT: A  400 GLN cc_start: 0.7453 (tp40) cc_final: 0.7082 (tp40)
REVERT: A  493 CYS cc_start: 0.7443 (m) cc_final: 0.7053 (t)
REVERT: A  558 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: A  560 TYR cc_start: 0.8091 (t80) cc_final: 0.7594 (t80)
REVERT: B  396 PRO cc_start: 0.6793 (Cg_exo) cc_final: 0.6395 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5371 (mmt-90) cc_final: 0.3993 (mtt90)
REVERT: B  400 GLN cc_start: 0.7487 (tp40) cc_final: 0.7164 (tp40)
REVERT: B  493 CYS cc_start: 0.7369 (m) cc_final: 0.6974 (t)
REVERT: B  558 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: B  560 TYR cc_start: 0.8114 (t80) cc_final: 0.7706 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1364
  time to fit residues: 40.4245
Evaluate side-chains
  187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
B 414 GLN
B 418 GLN
** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.119859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.099435 restraints weight = 15383.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.101371 restraints weight = 10402.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.103017 restraints weight = 8267.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6052  Z= 0.178
  Angle     :  0.645  13.448   8224  Z= 0.317
  Chirality :  0.038   0.134    988
  Planarity :  0.004   0.040    980
  Dihedral  :  3.422  12.839    796
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 26.81 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.31), residues: 710
  helix:  1.56 (0.20), residues: 612
  sheet:  None (None), residues: 0
  loop : -0.53 (0.63), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  76 
 HIS   0.004   0.001   HIS A 415 
 PHE   0.019   0.001   PHE A  79 
 TYR   0.015   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 366 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7373 (tt)
REVERT: A  167 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6260 (t0)
REVERT: A  396 PRO cc_start: 0.6882 (Cg_exo) cc_final: 0.6465 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5191 (mmt-90) cc_final: 0.3889 (mtt90)
REVERT: A  400 GLN cc_start: 0.7447 (tp40) cc_final: 0.7225 (tp40)
REVERT: A  493 CYS cc_start: 0.7498 (m) cc_final: 0.7061 (t)
REVERT: A  558 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: A  560 TYR cc_start: 0.8031 (t80) cc_final: 0.7735 (t80)
REVERT: B  107 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7389 (tt)
REVERT: B  396 PRO cc_start: 0.6768 (Cg_exo) cc_final: 0.6390 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5295 (mmt-90) cc_final: 0.4043 (mtt90)
REVERT: B  400 GLN cc_start: 0.7483 (tp40) cc_final: 0.7000 (tm-30)
REVERT: B  493 CYS cc_start: 0.7383 (m) cc_final: 0.6889 (t)
REVERT: B  560 TYR cc_start: 0.8004 (t80) cc_final: 0.7699 (t80)
  outliers start: 32
  outliers final: 19
  residues processed: 213
  average time/residue: 0.1382
  time to fit residues: 40.6495
Evaluate side-chains
  189 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  505 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
B 150 GLN
B 180 ASN
B 324 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.119149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.098532 restraints weight = 15821.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.100447 restraints weight = 10181.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.102194 restraints weight = 7910.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6052  Z= 0.187
  Angle     :  0.637  11.644   8224  Z= 0.319
  Chirality :  0.038   0.134    988
  Planarity :  0.004   0.045    980
  Dihedral  :  3.402  12.907    796
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 27.92 %
    Favored  : 67.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.31), residues: 710
  helix:  1.54 (0.20), residues: 610
  sheet:  None (None), residues: 0
  loop : -0.50 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  76 
 HIS   0.002   0.000   HIS A 415 
 PHE   0.018   0.002   PHE B  52 
 TYR   0.015   0.001   TYR A 311 
 ARG   0.002   0.000   ARG A 366 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7864 (mt)
REVERT: A  107 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7355 (tt)
REVERT: A  396 PRO cc_start: 0.6900 (Cg_exo) cc_final: 0.6463 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5267 (mmt-90) cc_final: 0.4043 (mtt90)
REVERT: A  400 GLN cc_start: 0.7626 (tp40) cc_final: 0.7305 (tp40)
REVERT: A  493 CYS cc_start: 0.7486 (m) cc_final: 0.7090 (t)
REVERT: A  558 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: A  560 TYR cc_start: 0.8071 (t80) cc_final: 0.7737 (t80)
REVERT: B   72 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7811 (mt)
REVERT: B  107 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7423 (tt)
REVERT: B  396 PRO cc_start: 0.6863 (Cg_exo) cc_final: 0.6470 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5435 (mmt-90) cc_final: 0.4214 (mtt90)
REVERT: B  493 CYS cc_start: 0.7454 (m) cc_final: 0.6933 (t)
REVERT: B  560 TYR cc_start: 0.8042 (t80) cc_final: 0.7747 (t80)
  outliers start: 29
  outliers final: 18
  residues processed: 212
  average time/residue: 0.1381
  time to fit residues: 40.9371
Evaluate side-chains
  197 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  504 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 ASN
B 414 GLN
B 418 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.118486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.098152 restraints weight = 15478.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.100409 restraints weight = 10045.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.101663 restraints weight = 7648.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6052  Z= 0.223
  Angle     :  0.683  17.348   8224  Z= 0.337
  Chirality :  0.039   0.128    988
  Planarity :  0.004   0.046    980
  Dihedral  :  3.435  16.260    796
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 28.71 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.30), residues: 710
  helix:  1.46 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.17 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 263 
 HIS   0.006   0.001   HIS B 194 
 PHE   0.021   0.002   PHE B  79 
 TYR   0.016   0.001   TYR A 548 
 ARG   0.009   0.000   ARG B  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.9222 (mt) cc_final: 0.9019 (mt)
REVERT: A  107 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7411 (tt)
REVERT: A  493 CYS cc_start: 0.7610 (m) cc_final: 0.7057 (t)
REVERT: A  558 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: B   72 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7873 (mt)
REVERT: B  107 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7458 (tt)
REVERT: B  396 PRO cc_start: 0.6947 (Cg_exo) cc_final: 0.6503 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5443 (mmt-90) cc_final: 0.4224 (mtt90)
REVERT: B  493 CYS cc_start: 0.7606 (m) cc_final: 0.7010 (t)
  outliers start: 35
  outliers final: 27
  residues processed: 206
  average time/residue: 0.1273
  time to fit residues: 37.2830
Evaluate side-chains
  196 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  505 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 522 ASN
B 414 GLN
B 418 GLN
B 522 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.118959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.098820 restraints weight = 15404.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.101175 restraints weight = 10014.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.102605 restraints weight = 7536.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6052  Z= 0.202
  Angle     :  0.701  14.711   8224  Z= 0.347
  Chirality :  0.039   0.137    988
  Planarity :  0.004   0.042    980
  Dihedral  :  3.487  15.900    796
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 32.97 %
    Favored  : 62.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.30), residues: 710
  helix:  1.31 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.41 (0.63), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  76 
 HIS   0.005   0.001   HIS B 194 
 PHE   0.023   0.002   PHE A  79 
 TYR   0.030   0.002   TYR A 560 
 ARG   0.006   0.000   ARG A  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 183
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7847 (mt)
REVERT: A  107 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: A  400 GLN cc_start: 0.7721 (tp40) cc_final: 0.7203 (tm-30)
REVERT: A  493 CYS cc_start: 0.7533 (m) cc_final: 0.7094 (t)
REVERT: A  558 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: B   72 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7794 (mt)
REVERT: B  107 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7408 (tt)
REVERT: B  560 TYR cc_start: 0.8133 (t80) cc_final: 0.7795 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 204
  average time/residue: 0.1189
  time to fit residues: 35.0641
Evaluate side-chains
  187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN
A 414 GLN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 ASN
B 180 ASN
B 239 GLN
B 414 GLN
B 418 GLN
B 522 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.119967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.100147 restraints weight = 15592.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.102527 restraints weight = 10069.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.103901 restraints weight = 7574.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6052  Z= 0.187
  Angle     :  0.723  15.171   8224  Z= 0.353
  Chirality :  0.040   0.175    988
  Planarity :  0.004   0.042    980
  Dihedral  :  3.465  14.807    796
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 33.44 %
    Favored  : 61.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.31), residues: 710
  helix:  1.31 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.50 (0.63), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 263 
 HIS   0.005   0.001   HIS B 194 
 PHE   0.022   0.002   PHE A  79 
 TYR   0.015   0.001   TYR B 548 
 ARG   0.003   0.000   ARG B  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 179
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.7122 (m-30) cc_final: 0.6909 (m-30)
REVERT: A   72 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7819 (mt)
REVERT: A  107 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7381 (tt)
REVERT: A  400 GLN cc_start: 0.7712 (tp40) cc_final: 0.7257 (tm-30)
REVERT: A  493 CYS cc_start: 0.7531 (m) cc_final: 0.7070 (t)
REVERT: A  560 TYR cc_start: 0.8197 (t80) cc_final: 0.7854 (t80)
REVERT: B   72 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7762 (mt)
REVERT: B  107 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7379 (tt)
REVERT: B  400 GLN cc_start: 0.7730 (tp40) cc_final: 0.7282 (tm-30)
REVERT: B  560 TYR cc_start: 0.8100 (t80) cc_final: 0.7789 (t80)
  outliers start: 34
  outliers final: 23
  residues processed: 200
  average time/residue: 0.1277
  time to fit residues: 36.3485
Evaluate side-chains
  189 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
B 414 GLN
B 522 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.118486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098370 restraints weight = 15666.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.100513 restraints weight = 10122.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.101720 restraints weight = 7790.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6052  Z= 0.273
  Angle     :  0.763  16.340   8224  Z= 0.376
  Chirality :  0.042   0.188    988
  Planarity :  0.004   0.040    980
  Dihedral  :  3.508  15.216    796
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 33.44 %
    Favored  : 61.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.31), residues: 710
  helix:  1.18 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.55 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 263 
 HIS   0.008   0.001   HIS A 415 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.015   0.002   TYR A 548 
 ARG   0.003   0.000   ARG B  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7877 (mt)
REVERT: A  107 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7489 (tt)
REVERT: A  324 GLN cc_start: 0.7196 (tp-100) cc_final: 0.6775 (tt0)
REVERT: A  400 GLN cc_start: 0.7748 (tp40) cc_final: 0.7176 (tm-30)
REVERT: A  493 CYS cc_start: 0.7570 (m) cc_final: 0.7135 (t)
REVERT: A  560 TYR cc_start: 0.8124 (t80) cc_final: 0.7777 (t80)
REVERT: B   72 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7846 (mt)
REVERT: B  107 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7428 (tt)
REVERT: B  400 GLN cc_start: 0.7815 (tp40) cc_final: 0.7311 (tm-30)
REVERT: B  560 TYR cc_start: 0.8086 (t80) cc_final: 0.7770 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 189
  average time/residue: 0.1218
  time to fit residues: 33.6905
Evaluate side-chains
  187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
A 522 ASN
B 414 GLN
B 522 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.119514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.099538 restraints weight = 15727.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.101420 restraints weight = 10186.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.103391 restraints weight = 7880.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6052  Z= 0.212
  Angle     :  0.766  16.595   8224  Z= 0.371
  Chirality :  0.042   0.161    988
  Planarity :  0.004   0.038    980
  Dihedral  :  3.524  14.487    796
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 34.54 %
    Favored  : 60.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.31), residues: 710
  helix:  1.22 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.62 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  76 
 HIS   0.006   0.001   HIS B 194 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.017   0.001   TYR A 548 
 ARG   0.002   0.000   ARG A  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7831 (mt)
REVERT: A  107 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7453 (tt)
REVERT: A  324 GLN cc_start: 0.7212 (tp-100) cc_final: 0.6769 (tt0)
REVERT: A  400 GLN cc_start: 0.7579 (tp40) cc_final: 0.7085 (tm-30)
REVERT: A  493 CYS cc_start: 0.7551 (m) cc_final: 0.7092 (t)
REVERT: A  560 TYR cc_start: 0.8128 (t80) cc_final: 0.7804 (t80)
REVERT: B   72 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7815 (mt)
REVERT: B  107 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7425 (tt)
REVERT: B  180 ASN cc_start: 0.8638 (m110) cc_final: 0.8356 (m110)
REVERT: B  560 TYR cc_start: 0.8043 (t80) cc_final: 0.7765 (t80)
  outliers start: 30
  outliers final: 23
  residues processed: 201
  average time/residue: 0.1140
  time to fit residues: 33.0542
Evaluate side-chains
  196 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 ASN
B 414 GLN
B 522 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.117887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098208 restraints weight = 15836.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.100313 restraints weight = 10179.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102068 restraints weight = 7769.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6052  Z= 0.256
  Angle     :  0.806  17.084   8224  Z= 0.394
  Chirality :  0.044   0.225    988
  Planarity :  0.004   0.040    980
  Dihedral  :  3.551  15.253    796
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 34.38 %
    Favored  : 60.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 710
  helix:  1.14 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.53 (0.66), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 263 
 HIS   0.005   0.001   HIS B 194 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.017   0.001   TYR B 152 
 ARG   0.002   0.000   ARG A  83 

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7883 (mt)
REVERT: A  107 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7428 (tt)
REVERT: A  400 GLN cc_start: 0.7580 (tp40) cc_final: 0.7130 (tm-30)
REVERT: A  493 CYS cc_start: 0.7575 (m) cc_final: 0.7131 (t)
REVERT: A  560 TYR cc_start: 0.8036 (t80) cc_final: 0.7706 (t80)
REVERT: B   72 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7872 (mt)
REVERT: B  107 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7451 (tt)
REVERT: B  180 ASN cc_start: 0.8658 (m110) cc_final: 0.8410 (m110)
REVERT: B  560 TYR cc_start: 0.7980 (t80) cc_final: 0.7716 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 189
  average time/residue: 0.1177
  time to fit residues: 32.2050
Evaluate side-chains
  198 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  124 TYR
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  522 ASN
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.117691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.098149 restraints weight = 15839.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.100006 restraints weight = 10168.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.101727 restraints weight = 7812.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.131   6052  Z= 0.346
  Angle     :  1.213  59.193   8224  Z= 0.697
  Chirality :  0.046   0.520    988
  Planarity :  0.007   0.136    980
  Dihedral  :  3.732  31.245    796
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 34.38 %
    Favored  : 60.88 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.31), residues: 710
  helix:  1.15 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.55 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 263 
 HIS   0.005   0.001   HIS A 415 
 PHE   0.022   0.002   PHE A 308 
 TYR   0.015   0.001   TYR B 548 
 ARG   0.002   0.000   ARG A  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1875.36 seconds
wall clock time: 34 minutes 36.02 seconds (2076.02 seconds total)