Starting phenix.real_space_refine
on Thu Jun  5 10:00:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug8_42217/06_2025/8ug8_42217.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug8_42217/06_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_42217/06_2025/8ug8_42217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug8_42217/06_2025/8ug8_42217.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug8_42217/06_2025/8ug8_42217.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug8_42217/06_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-5710/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: 5.04, per 1000 atoms: 0.85
  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: 1.31
  Conformation dependent library (CDL) restraints added in 637.8 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: 0.43
  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: 1.64

  Time building geometry restraints manager: 1.58 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:             1.770
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.970
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.010
-------------------------------------------------------------------------------
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= 0.205
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21364 (  468)
  hydrogen bonds       : angle       6.39598 ( 1392)
  covalent geometry    : bond        0.00314 ( 6052)
  covalent geometry    : angle       0.52735 ( 8224)

*********************** 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  : 0.693 
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: 0.1423
  time to fit residues: 43.2845
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  : 0.626 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 67 optimal weight:    0.2980
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.118823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.098660 restraints weight = 15480.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.100770 restraints weight = 10389.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.102123 restraints weight = 8075.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6052  Z= 0.167
  Angle     :  0.630   9.765   8224  Z= 0.326
  Chirality :  0.039   0.124    988
  Planarity :  0.005   0.047    980
  Dihedral  :  3.401  12.775    796
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 26.97 %
    Favored  : 69.09 %
  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:  1.96 (0.31), residues: 710
  helix:  1.62 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -0.35 (0.62), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  76 
 HIS   0.003   0.001   HIS B 415 
 PHE   0.022   0.002   PHE B  79 
 TYR   0.018   0.001   TYR B 124 
 ARG   0.003   0.000   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05444 (  468)
  hydrogen bonds       : angle       4.10261 ( 1392)
  covalent geometry    : bond        0.00334 ( 6052)
  covalent geometry    : angle       0.63010 ( 8224)

*********************** 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
  226 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  396 PRO cc_start: 0.6931 (Cg_exo) cc_final: 0.6486 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5356 (mmt-90) cc_final: 0.3918 (mtt90)
REVERT: A  400 GLN cc_start: 0.7524 (tp40) cc_final: 0.7135 (tp40)
REVERT: A  493 CYS cc_start: 0.7522 (m) cc_final: 0.7134 (t)
REVERT: A  558 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: A  560 TYR cc_start: 0.8121 (t80) cc_final: 0.7628 (t80)
REVERT: B  396 PRO cc_start: 0.6844 (Cg_exo) cc_final: 0.6421 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5511 (mmt-90) cc_final: 0.4142 (mtt90)
REVERT: B  400 GLN cc_start: 0.7546 (tp40) cc_final: 0.7213 (tp40)
REVERT: B  493 CYS cc_start: 0.7425 (m) cc_final: 0.7022 (t)
REVERT: B  558 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: B  560 TYR cc_start: 0.8147 (t80) cc_final: 0.7729 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 216
  average time/residue: 0.1306
  time to fit residues: 39.0447
Evaluate side-chains
  188 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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
B 180 ASN
B 324 GLN
B 418 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.118409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.097316 restraints weight = 15510.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.099481 restraints weight = 10168.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.101041 restraints weight = 7920.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2437

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= 0.156
  Angle     :  0.648  13.642   8224  Z= 0.320
  Chirality :  0.038   0.113    988
  Planarity :  0.004   0.039    980
  Dihedral  :  3.442  13.236    796
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  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:  1.83 (0.31), residues: 710
  helix:  1.51 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.21 (0.63), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  76 
 HIS   0.004   0.001   HIS A 415 
 PHE   0.017   0.002   PHE A  79 
 TYR   0.014   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04839 (  468)
  hydrogen bonds       : angle       4.04741 ( 1392)
  covalent geometry    : bond        0.00327 ( 6052)
  covalent geometry    : angle       0.64761 ( 8224)

*********************** 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
  218 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 186
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7424 (tt)
REVERT: A  167 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6267 (t0)
REVERT: A  396 PRO cc_start: 0.6932 (Cg_exo) cc_final: 0.6511 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5272 (mmt-90) cc_final: 0.3925 (mtt90)
REVERT: A  400 GLN cc_start: 0.7548 (tp40) cc_final: 0.7283 (tp40)
REVERT: A  493 CYS cc_start: 0.7515 (m) cc_final: 0.7122 (t)
REVERT: A  558 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8218 (tm-30)
REVERT: A  560 TYR cc_start: 0.8070 (t80) cc_final: 0.7725 (t80)
REVERT: B  107 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7458 (tt)
REVERT: B  396 PRO cc_start: 0.6828 (Cg_exo) cc_final: 0.6442 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5401 (mmt-90) cc_final: 0.4112 (mtt90)
REVERT: B  493 CYS cc_start: 0.7406 (m) cc_final: 0.6932 (t)
REVERT: B  560 TYR cc_start: 0.8055 (t80) cc_final: 0.7721 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 205
  average time/residue: 0.1453
  time to fit residues: 42.4618
Evaluate side-chains
  189 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
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  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   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:    0.0670
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
A 324 GLN
A 414 GLN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
B 414 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3990 r_free = 0.3990 target = 0.119662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.099287 restraints weight = 15803.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.101222 restraints weight = 10044.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.103255 restraints weight = 7740.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2766

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= 0.133
  Angle     :  0.631  11.608   8224  Z= 0.315
  Chirality :  0.038   0.138    988
  Planarity :  0.004   0.043    980
  Dihedral  :  3.417  12.887    796
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 28.86 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.55 (0.20), residues: 610
  sheet:  None (None), residues: 0
  loop : -0.53 (0.63), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  76 
 HIS   0.003   0.001   HIS B 415 
 PHE   0.018   0.002   PHE B  52 
 TYR   0.015   0.001   TYR A 311 
 ARG   0.002   0.000   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  468)
  hydrogen bonds       : angle       3.89049 ( 1392)
  covalent geometry    : bond        0.00279 ( 6052)
  covalent geometry    : angle       0.63104 ( 8224)

*********************** 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
  228 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LEU cc_start: 0.9210 (mt) cc_final: 0.8997 (mt)
REVERT: A   72 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7848 (mt)
REVERT: A  107 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7323 (tt)
REVERT: A  340 MET cc_start: 0.7845 (mtt) cc_final: 0.7625 (mtt)
REVERT: A  396 PRO cc_start: 0.6863 (Cg_exo) cc_final: 0.6437 (Cg_endo)
REVERT: A  397 ARG cc_start: 0.5199 (mmt-90) cc_final: 0.4028 (mtt90)
REVERT: A  400 GLN cc_start: 0.7632 (tp40) cc_final: 0.7083 (tm-30)
REVERT: A  493 CYS cc_start: 0.7500 (m) cc_final: 0.7073 (t)
REVERT: A  558 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: A  560 TYR cc_start: 0.7984 (t80) cc_final: 0.7713 (t80)
REVERT: B   31 LEU cc_start: 0.9274 (mt) cc_final: 0.9063 (mt)
REVERT: B   72 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7845 (mt)
REVERT: B  107 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (tt)
REVERT: B  180 ASN cc_start: 0.8636 (m110) cc_final: 0.8328 (m110)
REVERT: B  396 PRO cc_start: 0.6786 (Cg_exo) cc_final: 0.6415 (Cg_endo)
REVERT: B  397 ARG cc_start: 0.5359 (mmt-90) cc_final: 0.4176 (mtt90)
REVERT: B  493 CYS cc_start: 0.7475 (m) cc_final: 0.6986 (t)
REVERT: B  560 TYR cc_start: 0.8024 (t80) cc_final: 0.7758 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 214
  average time/residue: 0.1334
  time to fit residues: 40.3722
Evaluate side-chains
  196 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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  414 GLN
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:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 32 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0770
   chunk 41 optimal weight:    9.9990
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
A 418 GLN
A 522 ASN
B 239 GLN
B 414 GLN
B 418 GLN
B 522 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.120489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.100036 restraints weight = 15225.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.102235 restraints weight = 9895.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.103756 restraints weight = 7605.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6052  Z= 0.132
  Angle     :  0.646  11.122   8224  Z= 0.322
  Chirality :  0.038   0.128    988
  Planarity :  0.004   0.047    980
  Dihedral  :  3.401  12.608    796
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 29.65 %
    Favored  : 65.30 %
  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:  1.83 (0.31), residues: 710
  helix:  1.54 (0.20), residues: 610
  sheet:  None (None), residues: 0
  loop : -0.59 (0.62), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 263 
 HIS   0.005   0.001   HIS B 415 
 PHE   0.020   0.001   PHE B  52 
 TYR   0.013   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  468)
  hydrogen bonds       : angle       3.83468 ( 1392)
  covalent geometry    : bond        0.00269 ( 6052)
  covalent geometry    : angle       0.64592 ( 8224)

*********************** 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
  227 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.9216 (mt) cc_final: 0.8995 (mt)
REVERT: A   72 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7784 (mt)
REVERT: A  107 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7291 (tt)
REVERT: A  493 CYS cc_start: 0.7472 (m) cc_final: 0.6920 (t)
REVERT: A  560 TYR cc_start: 0.8052 (t80) cc_final: 0.7752 (t80)
REVERT: B   31 LEU cc_start: 0.9260 (mt) cc_final: 0.9039 (mt)
REVERT: B   72 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7793 (mt)
REVERT: B  107 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7415 (tt)
REVERT: B  180 ASN cc_start: 0.8561 (m110) cc_final: 0.8241 (m110)
REVERT: B  493 CYS cc_start: 0.7513 (m) cc_final: 0.6909 (t)
REVERT: B  560 TYR cc_start: 0.8095 (t80) cc_final: 0.7818 (t80)
  outliers start: 32
  outliers final: 23
  residues processed: 215
  average time/residue: 0.1198
  time to fit residues: 36.8048
Evaluate side-chains
  192 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 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  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   46 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  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 GLN
A 522 ASN
A 539 ASN
B 414 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 522 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.119818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.100127 restraints weight = 15501.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.102451 restraints weight = 9999.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.103961 restraints weight = 7518.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6052  Z= 0.144
  Angle     :  0.695  12.299   8224  Z= 0.344
  Chirality :  0.040   0.167    988
  Planarity :  0.004   0.047    980
  Dihedral  :  3.432  15.966    796
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 32.97 %
    Favored  : 62.30 %
  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:  1.75 (0.30), residues: 710
  helix:  1.51 (0.20), residues: 612
  sheet:  None (None), residues: 0
  loop : -0.86 (0.60), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 263 
 HIS   0.004   0.001   HIS B 194 
 PHE   0.023   0.002   PHE B  79 
 TYR   0.018   0.001   TYR A 152 
 ARG   0.007   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04326 (  468)
  hydrogen bonds       : angle       3.88958 ( 1392)
  covalent geometry    : bond        0.00300 ( 6052)
  covalent geometry    : angle       0.69538 ( 8224)

*********************** 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
  218 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.9225 (mt) cc_final: 0.9003 (mt)
REVERT: A   72 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7804 (mt)
REVERT: A  107 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7330 (tt)
REVERT: A  400 GLN cc_start: 0.7698 (tp40) cc_final: 0.7194 (tm-30)
REVERT: A  493 CYS cc_start: 0.7489 (m) cc_final: 0.7048 (t)
REVERT: B   31 LEU cc_start: 0.9251 (mt) cc_final: 0.9040 (mt)
REVERT: B   72 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7779 (mt)
REVERT: B  107 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7405 (tt)
REVERT: B  180 ASN cc_start: 0.8611 (m110) cc_final: 0.8263 (m110)
REVERT: B  493 CYS cc_start: 0.7501 (m) cc_final: 0.6979 (t)
  outliers start: 30
  outliers final: 22
  residues processed: 209
  average time/residue: 0.1253
  time to fit residues: 37.5924
Evaluate side-chains
  190 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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  414 GLN
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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3986 r_free = 0.3986 target = 0.119682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.099557 restraints weight = 15586.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.101545 restraints weight = 10099.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.103525 restraints weight = 7784.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3563

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= 0.154
  Angle     :  0.732  15.044   8224  Z= 0.361
  Chirality :  0.041   0.241    988
  Planarity :  0.004   0.046    980
  Dihedral  :  3.476  14.967    796
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 34.54 %
    Favored  : 60.57 %
  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:  1.54 (0.30), residues: 710
  helix:  1.33 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.47 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 263 
 HIS   0.007   0.001   HIS A 415 
 PHE   0.022   0.002   PHE B 247 
 TYR   0.013   0.001   TYR B 548 
 ARG   0.003   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04356 (  468)
  hydrogen bonds       : angle       4.09389 ( 1392)
  covalent geometry    : bond        0.00331 ( 6052)
  covalent geometry    : angle       0.73193 ( 8224)

*********************** 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
  208 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.7205 (m-30) cc_final: 0.6995 (m-30)
REVERT: A   72 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7837 (mt)
REVERT: A  107 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7341 (tt)
REVERT: A  400 GLN cc_start: 0.7697 (tp40) cc_final: 0.7202 (tm-30)
REVERT: A  493 CYS cc_start: 0.7568 (m) cc_final: 0.7073 (t)
REVERT: A  560 TYR cc_start: 0.8158 (t80) cc_final: 0.7875 (t80)
REVERT: B   72 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7808 (mt)
REVERT: B  107 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7422 (tt)
REVERT: B  180 ASN cc_start: 0.8645 (m110) cc_final: 0.8296 (m110)
REVERT: B  400 GLN cc_start: 0.7731 (tp40) cc_final: 0.7279 (tm-30)
REVERT: B  560 TYR cc_start: 0.8063 (t80) cc_final: 0.7768 (t80)
  outliers start: 31
  outliers final: 23
  residues processed: 197
  average time/residue: 0.1165
  time to fit residues: 33.4858
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  : 0.613 
-------------------------------------------------------------------------------
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   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  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   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:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3965 r_free = 0.3965 target = 0.118456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098481 restraints weight = 15685.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.100506 restraints weight = 10300.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.102117 restraints weight = 7973.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6052  Z= 0.190
  Angle     :  0.766  16.372   8224  Z= 0.381
  Chirality :  0.043   0.197    988
  Planarity :  0.004   0.039    980
  Dihedral  :  3.552  15.572    796
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 35.65 %
    Favored  : 58.83 %
  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:  1.31 (0.30), residues: 710
  helix:  1.18 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.61 (0.63), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 263 
 HIS   0.003   0.001   HIS A 415 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.014   0.001   TYR B 548 
 ARG   0.003   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  468)
  hydrogen bonds       : angle       4.21416 ( 1392)
  covalent geometry    : bond        0.00421 ( 6052)
  covalent geometry    : angle       0.76632 ( 8224)

*********************** 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
  205 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 0.678 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7888 (mt)
REVERT: A  107 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7438 (tt)
REVERT: A  324 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6785 (tt0)
REVERT: A  400 GLN cc_start: 0.7725 (tp40) cc_final: 0.7206 (tm-30)
REVERT: A  560 TYR cc_start: 0.8078 (t80) cc_final: 0.7789 (t80)
REVERT: B  107 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7455 (tt)
REVERT: B  180 ASN cc_start: 0.8698 (m110) cc_final: 0.8378 (m110)
REVERT: B  400 GLN cc_start: 0.7787 (tp40) cc_final: 0.7278 (tm-30)
REVERT: B  560 TYR cc_start: 0.8035 (t80) cc_final: 0.7704 (t80)
  outliers start: 35
  outliers final: 24
  residues processed: 195
  average time/residue: 0.1167
  time to fit residues: 33.0612
Evaluate side-chains
  194 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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   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  414 GLN
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   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
Chi-restraints excluded: chain B residue  539 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3992 r_free = 0.3992 target = 0.120015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.100345 restraints weight = 15602.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.102453 restraints weight = 10143.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.104172 restraints weight = 7771.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3727

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= 0.147
  Angle     :  0.778  16.220   8224  Z= 0.379
  Chirality :  0.042   0.186    988
  Planarity :  0.004   0.039    980
  Dihedral  :  3.571  14.808    796
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 35.96 %
    Favored  : 59.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.38 (0.30), residues: 710
  helix:  1.23 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.56 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 263 
 HIS   0.007   0.001   HIS A 415 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.015   0.001   TYR B 548 
 ARG   0.002   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  468)
  hydrogen bonds       : angle       4.22975 ( 1392)
  covalent geometry    : bond        0.00317 ( 6052)
  covalent geometry    : angle       0.77762 ( 8224)

*********************** 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
  202 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7854 (mt)
REVERT: A  107 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7343 (tt)
REVERT: A  324 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6960 (tt0)
REVERT: A  400 GLN cc_start: 0.7652 (tp40) cc_final: 0.7205 (tm-30)
REVERT: A  560 TYR cc_start: 0.8084 (t80) cc_final: 0.7850 (t80)
REVERT: B   72 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7824 (mt)
REVERT: B  107 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7405 (tt)
REVERT: B  180 ASN cc_start: 0.8630 (m110) cc_final: 0.8315 (m110)
REVERT: B  324 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6835 (tt0)
REVERT: B  560 TYR cc_start: 0.8002 (t80) cc_final: 0.7766 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 194
  average time/residue: 0.1131
  time to fit residues: 31.8588
Evaluate side-chains
  190 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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   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  414 GLN
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   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  414 GLN
Chi-restraints excluded: chain B residue  504 CYS
Chi-restraints excluded: chain B residue  522 ASN
Chi-restraints excluded: chain B residue  539 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 522 ASN
B 150 GLN
B 180 ASN
B 414 GLN

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 = 0.119373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.100392 restraints weight = 15730.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.102827 restraints weight = 9788.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.104562 restraints weight = 7232.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6052  Z= 0.153
  Angle     :  0.804  16.291   8224  Z= 0.391
  Chirality :  0.043   0.236    988
  Planarity :  0.004   0.039    980
  Dihedral  :  3.563  14.267    796
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 35.80 %
    Favored  : 60.09 %
  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:  1.38 (0.31), residues: 710
  helix:  1.22 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.48 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 263 
 HIS   0.004   0.001   HIS A 415 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.018   0.001   TYR B 152 
 ARG   0.002   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  468)
  hydrogen bonds       : angle       4.27296 ( 1392)
  covalent geometry    : bond        0.00330 ( 6052)
  covalent geometry    : angle       0.80373 ( 8224)

********************** 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
  190 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   72 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (mt)
REVERT: A  107 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7388 (tt)
REVERT: A  324 GLN cc_start: 0.7377 (tp-100) cc_final: 0.6999 (tt0)
REVERT: A  400 GLN cc_start: 0.7649 (tp40) cc_final: 0.7185 (tm-30)
REVERT: A  560 TYR cc_start: 0.8092 (t80) cc_final: 0.7877 (t80)
REVERT: B   72 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (mt)
REVERT: B  107 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7421 (tt)
REVERT: B  324 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6834 (tt0)
REVERT: B  560 TYR cc_start: 0.8012 (t80) cc_final: 0.7775 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 182
  average time/residue: 0.1317
  time to fit residues: 34.3516
Evaluate side-chains
  183 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
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   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  414 GLN
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   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  260 TYR
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 58 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0370
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 GLN
A 522 ASN
B 150 GLN
** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.120898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.101979 restraints weight = 15914.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.104373 restraints weight = 10026.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.105831 restraints weight = 7450.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3935

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= 0.144
  Angle     :  0.790  15.761   8224  Z= 0.385
  Chirality :  0.042   0.196    988
  Planarity :  0.004   0.039    980
  Dihedral  :  3.525  14.159    796
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 35.80 %
    Favored  : 60.57 %
  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:  1.47 (0.31), residues: 710
  helix:  1.26 (0.20), residues: 604
  sheet:  None (None), residues: 0
  loop : -0.37 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 263 
 HIS   0.007   0.001   HIS B 194 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.015   0.001   TYR B 548 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  468)
  hydrogen bonds       : angle       4.26371 ( 1392)
  covalent geometry    : bond        0.00298 ( 6052)
  covalent geometry    : angle       0.78970 ( 8224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2165.08 seconds
wall clock time: 39 minutes 7.74 seconds (2347.74 seconds total)