Starting phenix.real_space_refine
on Thu Jul 24 23:45:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x8w_33059/07_2025/7x8w_33059_trim.cif"
  }
  resolution = 3.1
  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: 5
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2186      2.51       5
     N     574      2.21       5
     O     682      1.98       5
     H    3214      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6674
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3065
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1883
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 1627
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 8, 'TRANS': 104}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 3.99, per 1000 atoms: 0.60
  Number of scatterers: 6674
  At special positions: 0
  Unit cell: (94.506, 63.004, 99.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     O     682      8.00
     N     574      7.00
     C    2186      6.00
     H    3214      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   6 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
      " NAG C   1 " - " ASN H  59 "
  Time building additional restraints: 2.19
  Conformation dependent library (CDL) restraints added in 574.8 milliseconds
  

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  788

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      10.1% alpha, 33.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.329A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.694A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.059A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 81 through 85
      removed outlier: 4.044A  pdb=" N   GLU L  85 " --> pdb=" O   ALA L  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.906A  pdb=" N   MET H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   TRP H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.871A  pdb=" N   TYR H 111 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.697A  pdb=" N   ALA L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TRP L  37 " --> pdb=" O   MET L  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.697A  pdb=" N   ALA L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA L  86 " --> pdb=" O   VAL L 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23

    109 hydrogen bonds defined for protein.
    258 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: 2.48

  Time building geometry restraints manager: 2.43 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 3214
        1.04 -     1.23: 82
        1.23 -     1.43: 1488
        1.43 -     1.62: 1954
        1.62 -     1.82: 24
  Bond restraints: 6762
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C1  MAN C   5 "
       pdb=" C2  MAN C   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.562 -0.036 2.00e-02 2.50e+03 3.33e+00
  bond pdb=" N   GLN L   1 "
       pdb=" CA  GLN L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.05e+00
  bond pdb=" N   GLN H   1 "
       pdb=" CA  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" N   GLN L   1 "
       pdb=" H   GLN L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.29e+00
  ... (remaining 6757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 11672
        1.32 -     2.64: 358
        2.64 -     3.96: 37
        3.96 -     5.28: 8
        5.28 -     6.60: 5
  Bond angle restraints: 12080
  Sorted by residual:
  angle pdb=" C3  BMA C   3 "
        pdb=" C2  BMA C   3 "
        pdb=" O2  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.35    6.60 3.00e+00 1.11e-01 4.85e+00
  angle pdb=" C3  MAN C   5 "
        pdb=" C2  MAN C   5 "
        pdb=" O2  MAN C   5 "
      ideal   model   delta    sigma   weight residual
     111.77  105.37    6.40 3.00e+00 1.11e-01 4.55e+00
  angle pdb=" C3  MAN C   4 "
        pdb=" C2  MAN C   4 "
        pdb=" O2  MAN C   4 "
      ideal   model   delta    sigma   weight residual
     111.77  105.65    6.12 3.00e+00 1.11e-01 4.16e+00
  angle pdb=" C4  FUC C   6 "
        pdb=" C3  FUC C   6 "
        pdb=" O3  FUC C   6 "
      ideal   model   delta    sigma   weight residual
     113.24  107.38    5.86 3.00e+00 1.11e-01 3.82e+00
  angle pdb=" C1  BMA C   3 "
        pdb=" O5  BMA C   3 "
        pdb=" C5  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     118.82  113.51    5.31 3.00e+00 1.11e-01 3.14e+00
  ... (remaining 12075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.68: 3140
       21.68 -    43.35: 166
       43.35 -    65.03: 54
       65.03 -    86.71: 16
       86.71 -   108.39: 5
  Dihedral angle restraints: 3381
    sinusoidal: 1856
      harmonic: 1525
  Sorted by residual:
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -179.68  108.39     1      3.00e+01 1.11e-03 1.40e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -58.69  106.31     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C6  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O4  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -163.34  -60.53 -102.81     1      3.00e+01 1.11e-03 1.30e+01
  ... (remaining 3378 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 459
       0.055 -    0.110: 68
       0.110 -    0.164: 12
       0.164 -    0.219: 0
       0.219 -    0.273: 2
  Chirality restraints: 541
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN H  59 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  ILE L  20 "
            pdb=" N   ILE L  20 "
            pdb=" C   ILE L  20 "
            pdb=" CB  ILE L  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  ... (remaining 538 not shown)

  Planarity restraints: 1023
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 106 "   -0.128 9.50e-02 1.11e+02   4.30e-02 2.23e+00
        pdb=" NE  ARG H 106 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 106 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 106 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG H 106 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG H 106 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG H 106 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 520 "   -0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A 521 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 521 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 521 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 400 "   -0.004 2.00e-02 2.50e+03   7.44e-03 5.54e-01
        pdb=" C   PHE A 400 "    0.013 2.00e-02 2.50e+03
        pdb=" O   PHE A 400 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   VAL A 401 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1020 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 616
        2.22 -     2.81: 13564
        2.81 -     3.41: 16199
        3.41 -     4.00: 23473
        4.00 -     4.60: 35091
  Nonbonded interactions: 88943
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  31 "
            pdb=" H   SER H 103 "
     model   vdw
     1.624 2.450
  nonbonded pdb=" O   THR A 345 "
            pdb="HH22 ARG A 509 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OD1 ASN A 360 "
            pdb=" HG1 THR A 523 "
     model   vdw
     1.655 2.450
  nonbonded pdb="HH21 ARG A 454 "
            pdb=" O   ASP A 467 "
     model   vdw
     1.674 2.450
  nonbonded pdb="HH11 ARG A 457 "
            pdb=" O   SER A 459 "
     model   vdw
     1.704 2.450
  ... (remaining 88938 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  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:             0.120
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.900
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
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      :  0.004   0.041   3562  Z= 0.191
  Angle     :  0.624   8.805   4861  Z= 0.285
  Chirality :  0.045   0.273    541
  Planarity :  0.004   0.056    611
  Dihedral  : 16.079 108.387   1376
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.40), residues: 429
  helix: -3.61 (0.73), residues: 27
  sheet:  0.25 (0.44), residues: 146
  loop : -1.32 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  36 
 HIS   0.001   0.001   HIS L  41 
 PHE   0.009   0.001   PHE A 347 
 TYR   0.008   0.001   TYR L  51 
 ARG   0.008   0.000   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       1.14619 (    6)
  link_ALPHA1-6        : bond        0.00703 (    1)
  link_ALPHA1-6        : angle       1.25012 (    3)
  link_BETA1-4         : bond        0.01299 (    3)
  link_BETA1-4         : angle       3.42673 (    9)
  link_ALPHA1-3        : bond        0.00197 (    1)
  link_ALPHA1-3        : angle       2.07110 (    3)
  hydrogen bonds       : bond        0.11363 (   99)
  hydrogen bonds       : angle       7.74662 (  258)
  link_BETA1-6         : bond        0.00616 (    1)
  link_BETA1-6         : angle       1.90046 (    3)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       0.85455 (   12)
  covalent geometry    : bond        0.00406 ( 3548)
  covalent geometry    : angle       0.60092 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.4645
  time to fit residues: 37.0962
Evaluate side-chains
  58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.1980
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.086556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.069966 restraints weight = 18497.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 3.33
r_work: 0.2751 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.0779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3562  Z= 0.110
  Angle     :  0.528   4.798   4861  Z= 0.256
  Chirality :  0.042   0.161    541
  Planarity :  0.004   0.036    611
  Dihedral  :  9.971  68.351    637
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.75 %
    Favored  : 93.97 %
  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 (0.40), residues: 429
  helix: -3.87 (0.65), residues: 32
  sheet:  0.63 (0.47), residues: 131
  loop : -1.32 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  41 
 PHE   0.005   0.001   PHE L 101 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.004   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00319 (    2)
  link_NAG-ASN         : angle       0.76457 (    6)
  link_ALPHA1-6        : bond        0.00719 (    1)
  link_ALPHA1-6        : angle       1.51735 (    3)
  link_BETA1-4         : bond        0.00730 (    3)
  link_BETA1-4         : angle       2.18911 (    9)
  link_ALPHA1-3        : bond        0.00808 (    1)
  link_ALPHA1-3        : angle       1.94818 (    3)
  hydrogen bonds       : bond        0.02628 (   99)
  hydrogen bonds       : angle       6.16082 (  258)
  link_BETA1-6         : bond        0.00556 (    1)
  link_BETA1-6         : angle       1.59211 (    3)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       1.19865 (   12)
  covalent geometry    : bond        0.00252 ( 3548)
  covalent geometry    : angle       0.51240 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.4916
  time to fit residues: 34.2779
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0870
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
L  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.067385 restraints weight = 18795.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.40
r_work: 0.2717 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.0961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3562  Z= 0.194
  Angle     :  0.537   6.491   4861  Z= 0.262
  Chirality :  0.042   0.170    541
  Planarity :  0.004   0.052    611
  Dihedral  :  8.877  58.196    637
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.53 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.22 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.40), residues: 429
  helix: -3.77 (0.72), residues: 32
  sheet: -0.03 (0.43), residues: 155
  loop : -1.28 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.001   0.001   HIS L  40 
 PHE   0.008   0.001   PHE A 347 
 TYR   0.008   0.001   TYR A 369 
 ARG   0.006   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    2)
  link_NAG-ASN         : angle       0.98412 (    6)
  link_ALPHA1-6        : bond        0.00550 (    1)
  link_ALPHA1-6        : angle       1.75244 (    3)
  link_BETA1-4         : bond        0.00581 (    3)
  link_BETA1-4         : angle       1.66351 (    9)
  link_ALPHA1-3        : bond        0.01052 (    1)
  link_ALPHA1-3        : angle       1.16808 (    3)
  hydrogen bonds       : bond        0.02725 (   99)
  hydrogen bonds       : angle       5.84841 (  258)
  link_BETA1-6         : bond        0.00292 (    1)
  link_BETA1-6         : angle       1.91073 (    3)
  SS BOND              : bond        0.00346 (    6)
  SS BOND              : angle       1.22050 (   12)
  covalent geometry    : bond        0.00440 ( 3548)
  covalent geometry    : angle       0.52495 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   73 ASP cc_start: 0.7468 (t0) cc_final: 0.7115 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.4780
  time to fit residues: 33.3475
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.068305 restraints weight = 18808.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.44
r_work: 0.2735 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3562  Z= 0.115
  Angle     :  0.520   7.010   4861  Z= 0.250
  Chirality :  0.042   0.212    541
  Planarity :  0.004   0.053    611
  Dihedral  :  8.001  57.916    637
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.36 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  9.04 %
    Favored  : 90.68 %
  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: -1.39 (0.41), residues: 429
  helix: -3.80 (0.69), residues: 32
  sheet:  0.39 (0.45), residues: 141
  loop : -1.34 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 
 PHE   0.005   0.001   PHE L 101 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.006   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    2)
  link_NAG-ASN         : angle       0.80261 (    6)
  link_ALPHA1-6        : bond        0.00434 (    1)
  link_ALPHA1-6        : angle       2.02940 (    3)
  link_BETA1-4         : bond        0.00565 (    3)
  link_BETA1-4         : angle       1.69795 (    9)
  link_ALPHA1-3        : bond        0.01069 (    1)
  link_ALPHA1-3        : angle       1.21864 (    3)
  hydrogen bonds       : bond        0.02420 (   99)
  hydrogen bonds       : angle       5.70743 (  258)
  link_BETA1-6         : bond        0.00519 (    1)
  link_BETA1-6         : angle       1.59427 (    3)
  SS BOND              : bond        0.00529 (    6)
  SS BOND              : angle       0.93431 (   12)
  covalent geometry    : bond        0.00264 ( 3548)
  covalent geometry    : angle       0.50856 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   73 ASP cc_start: 0.7452 (t0) cc_final: 0.7125 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 59
  average time/residue: 0.4730
  time to fit residues: 32.2924
Evaluate side-chains
  58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.4184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.085789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.068486 restraints weight = 18609.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.43
r_work: 0.2738 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3562  Z= 0.117
  Angle     :  0.514   6.966   4861  Z= 0.249
  Chirality :  0.042   0.207    541
  Planarity :  0.004   0.057    611
  Dihedral  :  7.433  57.253    637
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.13 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.04 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.40 (0.41), residues: 429
  helix: -3.78 (0.70), residues: 32
  sheet:  0.14 (0.44), residues: 152
  loop : -1.24 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 
 PHE   0.005   0.001   PHE A 400 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.006   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00236 (    2)
  link_NAG-ASN         : angle       0.81840 (    6)
  link_ALPHA1-6        : bond        0.00348 (    1)
  link_ALPHA1-6        : angle       2.05660 (    3)
  link_BETA1-4         : bond        0.00566 (    3)
  link_BETA1-4         : angle       1.61397 (    9)
  link_ALPHA1-3        : bond        0.01071 (    1)
  link_ALPHA1-3        : angle       1.17630 (    3)
  hydrogen bonds       : bond        0.02392 (   99)
  hydrogen bonds       : angle       5.60267 (  258)
  link_BETA1-6         : bond        0.00496 (    1)
  link_BETA1-6         : angle       1.56727 (    3)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       0.92103 (   12)
  covalent geometry    : bond        0.00270 ( 3548)
  covalent geometry    : angle       0.50367 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8143 (m-10)
REVERT: H   73 ASP cc_start: 0.7420 (t0) cc_final: 0.7095 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 61
  average time/residue: 0.4513
  time to fit residues: 32.1150
Evaluate side-chains
  59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.086044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.068860 restraints weight = 18620.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.41
r_work: 0.2745 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3562  Z= 0.103
  Angle     :  0.508   6.676   4861  Z= 0.247
  Chirality :  0.042   0.198    541
  Planarity :  0.004   0.057    611
  Dihedral  :  6.963  56.750    637
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.43 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.23 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.41), residues: 429
  helix: -3.78 (0.69), residues: 32
  sheet:  0.14 (0.44), residues: 152
  loop : -1.19 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 
 PHE   0.005   0.001   PHE L 101 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.006   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00246 (    2)
  link_NAG-ASN         : angle       0.78406 (    6)
  link_ALPHA1-6        : bond        0.00315 (    1)
  link_ALPHA1-6        : angle       2.03410 (    3)
  link_BETA1-4         : bond        0.00548 (    3)
  link_BETA1-4         : angle       1.58921 (    9)
  link_ALPHA1-3        : bond        0.01039 (    1)
  link_ALPHA1-3        : angle       1.14546 (    3)
  hydrogen bonds       : bond        0.02326 (   99)
  hydrogen bonds       : angle       5.52697 (  258)
  link_BETA1-6         : bond        0.00484 (    1)
  link_BETA1-6         : angle       1.45618 (    3)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       0.90079 (   12)
  covalent geometry    : bond        0.00238 ( 3548)
  covalent geometry    : angle       0.49824 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8262 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 59
  average time/residue: 0.4732
  time to fit residues: 32.8144
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0060
   chunk 9 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0170
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.8238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.086799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.069535 restraints weight = 18741.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 3.43
r_work: 0.2758 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3562  Z= 0.090
  Angle     :  0.496   6.353   4861  Z= 0.243
  Chirality :  0.042   0.178    541
  Planarity :  0.004   0.062    611
  Dihedral  :  6.605  56.413    637
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.96 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.51 %
    Favored  : 87.67 %
  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: -1.24 (0.41), residues: 429
  helix: -3.75 (0.70), residues: 32
  sheet:  0.37 (0.46), residues: 142
  loop : -1.14 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 
 PHE   0.008   0.001   PHE H  64 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.007   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    2)
  link_NAG-ASN         : angle       0.76880 (    6)
  link_ALPHA1-6        : bond        0.00285 (    1)
  link_ALPHA1-6        : angle       1.97165 (    3)
  link_BETA1-4         : bond        0.00544 (    3)
  link_BETA1-4         : angle       1.56448 (    9)
  link_ALPHA1-3        : bond        0.01053 (    1)
  link_ALPHA1-3        : angle       1.10336 (    3)
  hydrogen bonds       : bond        0.02226 (   99)
  hydrogen bonds       : angle       5.44479 (  258)
  link_BETA1-6         : bond        0.00527 (    1)
  link_BETA1-6         : angle       1.35495 (    3)
  SS BOND              : bond        0.00418 (    6)
  SS BOND              : angle       0.84564 (   12)
  covalent geometry    : bond        0.00210 ( 3548)
  covalent geometry    : angle       0.48676 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8269 (m-80)
REVERT: H   73 ASP cc_start: 0.7366 (t0) cc_final: 0.7071 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 63
  average time/residue: 0.4445
  time to fit residues: 32.5894
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.085958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.068531 restraints weight = 18803.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.44
r_work: 0.2737 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3562  Z= 0.144
  Angle     :  0.508   6.078   4861  Z= 0.248
  Chirality :  0.041   0.168    541
  Planarity :  0.004   0.062    611
  Dihedral  :  6.513  55.664    637
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.20 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.78 %
    Favored  : 87.40 %
  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: -1.35 (0.41), residues: 429
  helix: -3.80 (0.70), residues: 32
  sheet:  0.17 (0.44), residues: 152
  loop : -1.19 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.007   0.001   PHE A 347 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.007   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    2)
  link_NAG-ASN         : angle       0.87348 (    6)
  link_ALPHA1-6        : bond        0.00285 (    1)
  link_ALPHA1-6        : angle       1.92024 (    3)
  link_BETA1-4         : bond        0.00509 (    3)
  link_BETA1-4         : angle       1.49818 (    9)
  link_ALPHA1-3        : bond        0.01133 (    1)
  link_ALPHA1-3        : angle       1.07896 (    3)
  hydrogen bonds       : bond        0.02409 (   99)
  hydrogen bonds       : angle       5.45772 (  258)
  link_BETA1-6         : bond        0.00392 (    1)
  link_BETA1-6         : angle       1.64981 (    3)
  SS BOND              : bond        0.00425 (    6)
  SS BOND              : angle       0.81581 (   12)
  covalent geometry    : bond        0.00331 ( 3548)
  covalent geometry    : angle       0.49848 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8185 (m-10)
REVERT: H   73 ASP cc_start: 0.7411 (t0) cc_final: 0.7127 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 59
  average time/residue: 0.4480
  time to fit residues: 30.8281
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.067816 restraints weight = 18959.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.45
r_work: 0.2725 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3562  Z= 0.159
  Angle     :  0.520   5.750   4861  Z= 0.256
  Chirality :  0.041   0.156    541
  Planarity :  0.004   0.064    611
  Dihedral  :  6.489  55.279    637
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.43 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.05 %
    Favored  : 86.85 %
  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 (0.41), residues: 429
  helix: -3.79 (0.70), residues: 32
  sheet:  0.13 (0.44), residues: 152
  loop : -1.20 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  41 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.008   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00222 (    2)
  link_NAG-ASN         : angle       0.92451 (    6)
  link_ALPHA1-6        : bond        0.00336 (    1)
  link_ALPHA1-6        : angle       1.83053 (    3)
  link_BETA1-4         : bond        0.00454 (    3)
  link_BETA1-4         : angle       1.46665 (    9)
  link_ALPHA1-3        : bond        0.01077 (    1)
  link_ALPHA1-3        : angle       1.01482 (    3)
  hydrogen bonds       : bond        0.02481 (   99)
  hydrogen bonds       : angle       5.51172 (  258)
  link_BETA1-6         : bond        0.00435 (    1)
  link_BETA1-6         : angle       1.71797 (    3)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       0.87243 (   12)
  covalent geometry    : bond        0.00366 ( 3548)
  covalent geometry    : angle       0.51080 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8218 (m-10)
REVERT: H   73 ASP cc_start: 0.7467 (t0) cc_final: 0.7130 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 59
  average time/residue: 0.4498
  time to fit residues: 31.0744
Evaluate side-chains
  62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.086415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.068971 restraints weight = 18816.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.47
r_work: 0.2746 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3562  Z= 0.101
  Angle     :  0.505   5.412   4861  Z= 0.248
  Chirality :  0.041   0.152    541
  Planarity :  0.005   0.067    611
  Dihedral  :  6.368  55.385    637
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.73 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.60 %
    Favored  : 86.85 %
  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 (0.41), residues: 429
  helix: -3.79 (0.69), residues: 32
  sheet:  0.16 (0.44), residues: 152
  loop : -1.13 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 
 PHE   0.006   0.001   PHE A 400 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.008   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    2)
  link_NAG-ASN         : angle       0.84195 (    6)
  link_ALPHA1-6        : bond        0.00332 (    1)
  link_ALPHA1-6        : angle       1.76042 (    3)
  link_BETA1-4         : bond        0.00484 (    3)
  link_BETA1-4         : angle       1.52083 (    9)
  link_ALPHA1-3        : bond        0.01102 (    1)
  link_ALPHA1-3        : angle       1.07472 (    3)
  hydrogen bonds       : bond        0.02368 (   99)
  hydrogen bonds       : angle       5.46834 (  258)
  link_BETA1-6         : bond        0.00572 (    1)
  link_BETA1-6         : angle       1.41359 (    3)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.76589 (   12)
  covalent geometry    : bond        0.00236 ( 3548)
  covalent geometry    : angle       0.49616 ( 4825)

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

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

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  858 Ramachandran restraints generated.
    429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8338 (m-80)
REVERT: H   73 ASP cc_start: 0.7400 (t0) cc_final: 0.7101 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 61
  average time/residue: 0.4960
  time to fit residues: 35.0901
Evaluate side-chains
  61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain H residue   60 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.087001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.069564 restraints weight = 18642.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 3.47
r_work: 0.2759 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3562  Z= 0.090
  Angle     :  0.494   4.868   4861  Z= 0.244
  Chirality :  0.041   0.155    541
  Planarity :  0.004   0.059    611
  Dihedral  :  6.197  55.243    637
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.96 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.33 %
    Favored  : 86.85 %
  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: -1.21 (0.41), residues: 429
  helix: -3.78 (0.70), residues: 32
  sheet:  0.24 (0.44), residues: 152
  loop : -1.06 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS L  41 
 PHE   0.005   0.001   PHE A 400 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.008   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    2)
  link_NAG-ASN         : angle       0.78950 (    6)
  link_ALPHA1-6        : bond        0.00323 (    1)
  link_ALPHA1-6        : angle       1.73226 (    3)
  link_BETA1-4         : bond        0.00496 (    3)
  link_BETA1-4         : angle       1.53716 (    9)
  link_ALPHA1-3        : bond        0.01096 (    1)
  link_ALPHA1-3        : angle       1.10833 (    3)
  hydrogen bonds       : bond        0.02298 (   99)
  hydrogen bonds       : angle       5.37716 (  258)
  link_BETA1-6         : bond        0.00535 (    1)
  link_BETA1-6         : angle       1.28688 (    3)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       0.74903 (   12)
  covalent geometry    : bond        0.00211 ( 3548)
  covalent geometry    : angle       0.48553 ( 4825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4049.46 seconds
wall clock time: 70 minutes 22.36 seconds (4222.36 seconds total)