Starting phenix.real_space_refine
on Sat Apr 26 23:20:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yrj_39543/04_2025/8yrj_39543.cif"
  }
  resolution = 3.87
  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=   0.006
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      21      5.16       5
     C    2442      2.51       5
     N     597      2.21       5
     O     688      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-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3748
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1743
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208}
    Chain: "G"
      Number of atoms: 297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 297
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "H"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 341
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 1, 'TRANS': 41}
    Chain: "B"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1247
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 1, 'TRANS': 158}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.22, per 1000 atoms: 0.86
  Number of scatterers: 3748
  At special positions: 0
  Unit cell: (57.27, 74.7, 118.69, 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      21     16.00
     O     688      8.00
     N     597      7.00
     C    2442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  25 " - pdb=" SG  CYS H  25 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 163 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A 301 " - " ASN A  73 "
      " NAG A 302 " - " ASN A 167 "
      " NAG A 303 " - " ASN A 152 "
      " NAG C   1 " - " ASN A  66 "
      " NAG D   1 " - " ASN A 106 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 390.8 milliseconds
  

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  858

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 6 sheets defined
      56.2% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 236
    Processing helix  chain 'G' and resid 23 through 58
    Processing helix  chain 'H' and resid 21 through 62
      removed outlier: 3.945A  pdb=" N   CYS H  25 " --> pdb=" O   GLU H  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 75
      removed outlier: 5.267A  pdb=" N   LYS B  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   LYS B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLU B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 111
    Processing helix  chain 'B' and resid 117 through 154
      removed outlier: 4.115A  pdb=" N   GLY B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 199
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 3.638A  pdb=" N   THR A 108 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121
      removed outlier: 4.289A  pdb=" N   TYR A 177 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   LYS A 141 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   TYR A 153 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   TYR A 144 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.766A  pdb=" N   GLY A 125 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   PHE A 127 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   ARG A 162 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1124
        1.35 -     1.46: 980
        1.46 -     1.58: 1692
        1.58 -     1.70: 0
        1.70 -     1.82: 27
  Bond restraints: 3823
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.551 -0.032 2.00e-02 2.50e+03 2.58e+00
  bond pdb=" C1  NAG A 302 "
       pdb=" O5  NAG A 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.55e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.20e+00
  ... (remaining 3818 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 5021
        1.24 -     2.47: 117
        2.47 -     3.71: 24
        3.71 -     4.95: 12
        4.95 -     6.18: 9
  Bond angle restraints: 5183
  Sorted by residual:
  angle pdb=" C   CYS A 198 "
        pdb=" N   LYS A 199 "
        pdb=" CA  LYS A 199 "
      ideal   model   delta    sigma   weight residual
     121.54  126.03   -4.49 1.91e+00 2.74e-01 5.53e+00
  angle pdb=" C   GLN B  40 "
        pdb=" N   THR B  41 "
        pdb=" CA  THR B  41 "
      ideal   model   delta    sigma   weight residual
     121.54  125.78   -4.24 1.91e+00 2.74e-01 4.93e+00
  angle pdb=" N   GLU H  21 "
        pdb=" CA  GLU H  21 "
        pdb=" C   GLU H  21 "
      ideal   model   delta    sigma   weight residual
     109.81  114.50   -4.69 2.21e+00 2.05e-01 4.50e+00
  angle pdb=" C3  BMA C   3 "
        pdb=" C2  BMA C   3 "
        pdb=" O2  BMA C   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.77    6.18 3.00e+00 1.11e-01 4.25e+00
  angle pdb=" C3  BMA D   3 "
        pdb=" C2  BMA D   3 "
        pdb=" O2  BMA D   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.79    6.16 3.00e+00 1.11e-01 4.22e+00
  ... (remaining 5178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.39: 2161
       23.39 -    46.78: 161
       46.78 -    70.17: 25
       70.17 -    93.56: 17
       93.56 -   116.95: 11
  Dihedral angle restraints: 2375
    sinusoidal: 1042
      harmonic: 1333
  Sorted by residual:
  dihedral pdb=" CB  CYS G  25 "
           pdb=" SG  CYS G  25 "
           pdb=" SG  CYS H  25 "
           pdb=" CB  CYS H  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.20  -81.20     1      1.00e+01 1.00e-02 8.13e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   52.84 -116.95     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C6  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -72.39 -116.45     1      3.00e+01 1.11e-03 1.54e+01
  ... (remaining 2372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 540
       0.054 -    0.108: 82
       0.108 -    0.161: 14
       0.161 -    0.215: 0
       0.215 -    0.269: 2
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.81e+00
  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   -2.54    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" C2  BMA C   3 "
            pdb=" C1  BMA C   3 "
            pdb=" C3  BMA C   3 "
            pdb=" O2  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 635 not shown)

  Planarity restraints: 620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 207 "   -0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 208 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 208 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 208 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 157 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO A 158 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 158 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 158 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  56 "   -0.005 2.00e-02 2.50e+03   9.38e-03 8.79e-01
        pdb=" C   GLN A  56 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLN A  56 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   MET A  57 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 617 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 654
        2.77 -     3.30: 3630
        3.30 -     3.84: 6313
        3.84 -     4.37: 6566
        4.37 -     4.90: 11859
  Nonbonded interactions: 29022
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 168 "
            pdb=" OH  TYR A 172 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" N   TRP B  42 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OG  SER A 154 "
            pdb=" O   SER A 157 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   LEU A 221 "
            pdb=" OG1 THR A 225 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" O   ASP A  86 "
            pdb=" OH  TYR A  90 "
     model   vdw
     2.375 3.040
  ... (remaining 29017 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'H' and resid 22 through 58)
}

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:             1.930
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.330
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
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   0.083   3836  Z= 0.170
  Angle     :  0.569   6.185   5218  Z= 0.262
  Chirality :  0.042   0.269    638
  Planarity :  0.003   0.033    615
  Dihedral  : 19.292 116.955   1505
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  3.59 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.39 (0.42), residues: 446
  helix:  3.31 (0.31), residues: 232
  sheet:  0.83 (0.61), residues: 71
  loop : -1.08 (0.58), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  42 
 HIS   0.001   0.000   HIS A 173 
 PHE   0.006   0.001   PHE B 168 
 TYR   0.007   0.001   TYR A  50 
 ARG   0.001   0.000   ARG A 162 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00353 (    5)
  link_NAG-ASN         : angle       2.80331 (   15)
  link_BETA1-4         : bond        0.00844 (    4)
  link_BETA1-4         : angle       1.95186 (   12)
  hydrogen bonds       : bond        0.10320 (  251)
  hydrogen bonds       : angle       4.01228 (  732)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       0.90827 (    8)
  covalent geometry    : bond        0.00326 ( 3823)
  covalent geometry    : angle       0.54169 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8195 (tttt) cc_final: 0.7872 (ttpt)
REVERT: A   93 GLN cc_start: 0.7156 (tt0) cc_final: 0.6787 (tm-30)
REVERT: A  128 ASP cc_start: 0.8230 (m-30) cc_final: 0.7993 (m-30)
REVERT: A  144 TYR cc_start: 0.7097 (m-80) cc_final: 0.6446 (m-80)
REVERT: A  203 LEU cc_start: 0.9533 (mt) cc_final: 0.9281 (mt)
REVERT: H   33 PHE cc_start: 0.8736 (t80) cc_final: 0.8306 (t80)
REVERT: B  109 ILE cc_start: 0.9025 (mm) cc_final: 0.8642 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1681
  time to fit residues: 38.6587
Evaluate side-chains
  125 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.182055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.156994 restraints weight = 7675.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.160896 restraints weight = 4726.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163624 restraints weight = 3318.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3836  Z= 0.175
  Angle     :  0.893  16.918   5218  Z= 0.406
  Chirality :  0.050   0.298    638
  Planarity :  0.004   0.035    615
  Dihedral  : 14.815  84.794    677
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.95 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 (0.40), residues: 446
  helix:  3.00 (0.31), residues: 226
  sheet: -0.08 (0.63), residues: 68
  loop : -1.03 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 137 
 HIS   0.008   0.002   HIS A 173 
 PHE   0.030   0.002   PHE B  45 
 TYR   0.043   0.002   TYR H  26 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01763 (    5)
  link_NAG-ASN         : angle       7.52892 (   15)
  link_BETA1-4         : bond        0.01131 (    4)
  link_BETA1-4         : angle       3.03338 (   12)
  hydrogen bonds       : bond        0.04212 (  251)
  hydrogen bonds       : angle       3.87081 (  732)
  SS BOND              : bond        0.00569 (    4)
  SS BOND              : angle       2.89270 (    8)
  covalent geometry    : bond        0.00363 ( 3823)
  covalent geometry    : angle       0.77794 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8172 (p90) cc_final: 0.7769 (p90)
REVERT: A  137 TRP cc_start: 0.7140 (m-10) cc_final: 0.6620 (m-10)
REVERT: A  144 TYR cc_start: 0.7102 (m-80) cc_final: 0.6766 (m-10)
REVERT: A  222 LEU cc_start: 0.8701 (tt) cc_final: 0.8123 (tp)
REVERT: H   33 PHE cc_start: 0.8825 (t80) cc_final: 0.8389 (t80)
REVERT: H   37 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8581 (mm)
REVERT: B   51 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8080 (mm-30)
REVERT: B   79 ASP cc_start: 0.8414 (m-30) cc_final: 0.8166 (p0)
  outliers start: 18
  outliers final: 11
  residues processed: 141
  average time/residue: 0.1414
  time to fit residues: 24.6048
Evaluate side-chains
  130 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.176603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.151477 restraints weight = 7660.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155364 restraints weight = 4689.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.158029 restraints weight = 3305.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3836  Z= 0.159
  Angle     :  0.855  14.432   5218  Z= 0.390
  Chirality :  0.047   0.213    638
  Planarity :  0.003   0.031    615
  Dihedral  : 10.472  58.169    677
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.69 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.57 (0.40), residues: 446
  helix:  2.51 (0.32), residues: 235
  sheet:  0.57 (0.65), residues: 67
  loop : -1.32 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 134 
 HIS   0.006   0.001   HIS A  65 
 PHE   0.010   0.002   PHE B  45 
 TYR   0.024   0.002   TYR H  26 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01241 (    5)
  link_NAG-ASN         : angle       6.21242 (   15)
  link_BETA1-4         : bond        0.00920 (    4)
  link_BETA1-4         : angle       3.51835 (   12)
  hydrogen bonds       : bond        0.04222 (  251)
  hydrogen bonds       : angle       3.83992 (  732)
  SS BOND              : bond        0.00742 (    4)
  SS BOND              : angle       2.53696 (    8)
  covalent geometry    : bond        0.00331 ( 3823)
  covalent geometry    : angle       0.76540 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.7652 (tt0) cc_final: 0.7029 (tm-30)
REVERT: A  127 PHE cc_start: 0.8363 (p90) cc_final: 0.7979 (p90)
REVERT: A  144 TYR cc_start: 0.7084 (m-80) cc_final: 0.6722 (m-10)
REVERT: H   33 PHE cc_start: 0.8697 (t80) cc_final: 0.8491 (t80)
REVERT: B   79 ASP cc_start: 0.8456 (m-30) cc_final: 0.8210 (p0)
  outliers start: 15
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1383
  time to fit residues: 24.0517
Evaluate side-chains
  130 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.178193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.151291 restraints weight = 7559.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.155362 restraints weight = 4458.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.158195 restraints weight = 3094.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3836  Z= 0.171
  Angle     :  0.830  13.863   5218  Z= 0.381
  Chirality :  0.047   0.218    638
  Planarity :  0.003   0.030    615
  Dihedral  :  8.034  57.862    677
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.71 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.44 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.37 (0.40), residues: 446
  helix:  2.47 (0.32), residues: 234
  sheet:  0.11 (0.67), residues: 60
  loop : -1.34 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 137 
 HIS   0.002   0.001   HIS A 132 
 PHE   0.024   0.002   PHE A  40 
 TYR   0.021   0.002   TYR H  26 
 ARG   0.003   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01177 (    5)
  link_NAG-ASN         : angle       5.90697 (   15)
  link_BETA1-4         : bond        0.00873 (    4)
  link_BETA1-4         : angle       3.70669 (   12)
  hydrogen bonds       : bond        0.04289 (  251)
  hydrogen bonds       : angle       3.90162 (  732)
  SS BOND              : bond        0.00700 (    4)
  SS BOND              : angle       1.77846 (    8)
  covalent geometry    : bond        0.00368 ( 3823)
  covalent geometry    : angle       0.74565 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8431 (p90) cc_final: 0.8068 (p90)
REVERT: A  135 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8147 (tptp)
REVERT: A  144 TYR cc_start: 0.7072 (m-80) cc_final: 0.6713 (m-10)
REVERT: H   33 PHE cc_start: 0.8760 (t80) cc_final: 0.7630 (t80)
REVERT: B   79 ASP cc_start: 0.8523 (m-30) cc_final: 0.8224 (p0)
REVERT: B  103 SER cc_start: 0.8052 (m) cc_final: 0.7769 (m)
REVERT: B  175 MET cc_start: 0.8108 (mmm) cc_final: 0.7838 (mmm)
  outliers start: 16
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1403
  time to fit residues: 24.9766
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0170
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.1424

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.173062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.147060 restraints weight = 7625.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150941 restraints weight = 4438.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.153673 restraints weight = 3075.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.5486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3836  Z= 0.189
  Angle     :  0.847  13.599   5218  Z= 0.397
  Chirality :  0.048   0.226    638
  Planarity :  0.003   0.038    615
  Dihedral  :  7.084  57.047    677
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.26 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.94 %
    Favored  : 70.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.50 (0.40), residues: 446
  helix:  2.61 (0.32), residues: 224
  sheet:  0.13 (0.69), residues: 56
  loop : -1.01 (0.51), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  95 
 HIS   0.003   0.001   HIS A  65 
 PHE   0.014   0.002   PHE A  40 
 TYR   0.016   0.002   TYR B 193 
 ARG   0.002   0.000   ARG A 162 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01005 (    5)
  link_NAG-ASN         : angle       5.89155 (   15)
  link_BETA1-4         : bond        0.00620 (    4)
  link_BETA1-4         : angle       3.55956 (   12)
  hydrogen bonds       : bond        0.04523 (  251)
  hydrogen bonds       : angle       3.93063 (  732)
  SS BOND              : bond        0.00757 (    4)
  SS BOND              : angle       1.48314 (    8)
  covalent geometry    : bond        0.00398 ( 3823)
  covalent geometry    : angle       0.76712 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8073 (m-10) cc_final: 0.7727 (m-10)
REVERT: A  127 PHE cc_start: 0.8447 (p90) cc_final: 0.8126 (p90)
REVERT: A  135 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8122 (tptp)
REVERT: A  144 TYR cc_start: 0.7137 (m-80) cc_final: 0.6667 (m-10)
REVERT: A  218 ASP cc_start: 0.7217 (t0) cc_final: 0.6896 (t0)
REVERT: H   33 PHE cc_start: 0.8696 (t80) cc_final: 0.7727 (t80)
REVERT: B  148 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.5978 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1370
  time to fit residues: 24.2861
Evaluate side-chains
  143 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.173661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.147262 restraints weight = 7386.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.151211 restraints weight = 4356.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.153853 restraints weight = 3008.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.5783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3836  Z= 0.158
  Angle     :  0.818  13.345   5218  Z= 0.382
  Chirality :  0.047   0.256    638
  Planarity :  0.003   0.033    615
  Dihedral  :  6.784  57.287    677
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 25.94 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.48 (0.40), residues: 446
  helix:  2.50 (0.32), residues: 222
  sheet:  0.30 (0.70), residues: 55
  loop : -0.90 (0.51), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  95 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.021   0.002   PHE H  33 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.001   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01088 (    5)
  link_NAG-ASN         : angle       5.70420 (   15)
  link_BETA1-4         : bond        0.00803 (    4)
  link_BETA1-4         : angle       3.42672 (   12)
  hydrogen bonds       : bond        0.04420 (  251)
  hydrogen bonds       : angle       3.93677 (  732)
  SS BOND              : bond        0.00612 (    4)
  SS BOND              : angle       1.81813 (    8)
  covalent geometry    : bond        0.00333 ( 3823)
  covalent geometry    : angle       0.73955 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8076 (m-10) cc_final: 0.7734 (m-10)
REVERT: A  127 PHE cc_start: 0.8365 (p90) cc_final: 0.8079 (p90)
REVERT: A  135 LYS cc_start: 0.8277 (ttpt) cc_final: 0.8071 (tptp)
REVERT: A  144 TYR cc_start: 0.7018 (m-80) cc_final: 0.6463 (m-10)
REVERT: A  203 LEU cc_start: 0.9593 (mt) cc_final: 0.9355 (mt)
REVERT: A  204 GLN cc_start: 0.8452 (tt0) cc_final: 0.7923 (tp40)
REVERT: A  218 ASP cc_start: 0.7224 (t0) cc_final: 0.6816 (t0)
REVERT: B  103 SER cc_start: 0.8163 (m) cc_final: 0.7914 (m)
REVERT: B  148 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.5951 (t80)
REVERT: B  193 TYR cc_start: 0.7808 (t80) cc_final: 0.7537 (t80)
  outliers start: 22
  outliers final: 18
  residues processed: 143
  average time/residue: 0.1362
  time to fit residues: 24.6748
Evaluate side-chains
  144 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   46 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 15 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.168908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.142254 restraints weight = 7578.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.146022 restraints weight = 4507.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.148618 restraints weight = 3163.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.6345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3836  Z= 0.204
  Angle     :  0.861  12.376   5218  Z= 0.406
  Chirality :  0.048   0.241    638
  Planarity :  0.004   0.032    615
  Dihedral  :  6.821  55.849    677
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 27.68 %
    Favored  : 65.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.03 (0.40), residues: 446
  helix:  2.05 (0.32), residues: 225
  sheet:  0.16 (0.68), residues: 56
  loop : -1.08 (0.51), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 202 
 HIS   0.003   0.001   HIS A  65 
 PHE   0.013   0.002   PHE B  52 
 TYR   0.014   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00922 (    5)
  link_NAG-ASN         : angle       5.56253 (   15)
  link_BETA1-4         : bond        0.00612 (    4)
  link_BETA1-4         : angle       3.29158 (   12)
  hydrogen bonds       : bond        0.04851 (  251)
  hydrogen bonds       : angle       4.18360 (  732)
  SS BOND              : bond        0.00716 (    4)
  SS BOND              : angle       1.39116 (    8)
  covalent geometry    : bond        0.00441 ( 3823)
  covalent geometry    : angle       0.79250 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8153 (m-10) cc_final: 0.7618 (m-10)
REVERT: A  127 PHE cc_start: 0.8430 (p90) cc_final: 0.8161 (p90)
REVERT: A  204 GLN cc_start: 0.8397 (tt0) cc_final: 0.7923 (tp40)
REVERT: B  103 SER cc_start: 0.8335 (m) cc_final: 0.8087 (m)
  outliers start: 26
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1246
  time to fit residues: 23.5345
Evaluate side-chains
  150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  107 SER
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.164670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.138248 restraints weight = 7620.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141822 restraints weight = 4632.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144315 restraints weight = 3295.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.6893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   3836  Z= 0.233
  Angle     :  0.910  12.557   5218  Z= 0.435
  Chirality :  0.049   0.266    638
  Planarity :  0.004   0.031    615
  Dihedral  :  7.108  56.253    677
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.16 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 29.93 %
    Favored  : 64.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.64 (0.39), residues: 446
  helix:  1.75 (0.31), residues: 225
  sheet: -0.25 (0.66), residues: 56
  loop : -1.20 (0.52), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  95 
 HIS   0.003   0.001   HIS A  65 
 PHE   0.022   0.002   PHE H  33 
 TYR   0.021   0.002   TYR B  92 
 ARG   0.003   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00865 (    5)
  link_NAG-ASN         : angle       5.47125 (   15)
  link_BETA1-4         : bond        0.00596 (    4)
  link_BETA1-4         : angle       3.28404 (   12)
  hydrogen bonds       : bond        0.05085 (  251)
  hydrogen bonds       : angle       4.33192 (  732)
  SS BOND              : bond        0.00716 (    4)
  SS BOND              : angle       1.51361 (    8)
  covalent geometry    : bond        0.00516 ( 3823)
  covalent geometry    : angle       0.84731 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8282 (m-10) cc_final: 0.7689 (m-10)
REVERT: A  204 GLN cc_start: 0.8496 (tt0) cc_final: 0.8137 (tp40)
REVERT: B  148 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6008 (t80)
  outliers start: 24
  outliers final: 21
  residues processed: 150
  average time/residue: 0.1257
  time to fit residues: 23.8896
Evaluate side-chains
  154 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  124 HIS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   29 ASP
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 PHE
Chi-restraints excluded: chain B residue  167 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.141698 restraints weight = 7697.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.145402 restraints weight = 4717.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.147981 restraints weight = 3366.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.7051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3836  Z= 0.177
  Angle     :  0.892  12.653   5218  Z= 0.429
  Chirality :  0.049   0.293    638
  Planarity :  0.003   0.028    615
  Dihedral  :  6.935  55.894    677
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.16 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 33.42 %
    Favored  : 63.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.70 (0.40), residues: 446
  helix:  1.81 (0.31), residues: 225
  sheet: -0.33 (0.64), residues: 63
  loop : -1.18 (0.53), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 137 
 HIS   0.002   0.001   HIS A 124 
 PHE   0.031   0.002   PHE A 127 
 TYR   0.020   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01002 (    5)
  link_NAG-ASN         : angle       5.12983 (   15)
  link_BETA1-4         : bond        0.00822 (    4)
  link_BETA1-4         : angle       3.15741 (   12)
  hydrogen bonds       : bond        0.04767 (  251)
  hydrogen bonds       : angle       4.40979 (  732)
  SS BOND              : bond        0.00621 (    4)
  SS BOND              : angle       1.22447 (    8)
  covalent geometry    : bond        0.00402 ( 3823)
  covalent geometry    : angle       0.83637 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8188 (m-10) cc_final: 0.7664 (m-10)
REVERT: A  204 GLN cc_start: 0.8450 (tt0) cc_final: 0.8176 (tp40)
REVERT: A  236 GLN cc_start: 0.7486 (tm-30) cc_final: 0.6129 (tt0)
REVERT: H   52 LYS cc_start: 0.9138 (mmtm) cc_final: 0.8591 (mmmt)
REVERT: B   51 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7831 (mt-10)
REVERT: B  148 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6050 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1312
  time to fit residues: 22.9149
Evaluate side-chains
  140 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.165912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.137082 restraints weight = 8150.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.140944 restraints weight = 4957.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.143748 restraints weight = 3528.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.7204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   3836  Z= 0.200
  Angle     :  0.937  13.731   5218  Z= 0.450
  Chirality :  0.051   0.329    638
  Planarity :  0.004   0.028    615
  Dihedral  :  7.069  54.147    677
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.38 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 33.17 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.62 (0.39), residues: 446
  helix:  1.80 (0.31), residues: 225
  sheet: -0.26 (0.61), residues: 70
  loop : -1.40 (0.52), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  95 
 HIS   0.004   0.001   HIS A 132 
 PHE   0.049   0.002   PHE A 127 
 TYR   0.021   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00882 (    5)
  link_NAG-ASN         : angle       5.10374 (   15)
  link_BETA1-4         : bond        0.00661 (    4)
  link_BETA1-4         : angle       3.13781 (   12)
  hydrogen bonds       : bond        0.04779 (  251)
  hydrogen bonds       : angle       4.44189 (  732)
  SS BOND              : bond        0.00822 (    4)
  SS BOND              : angle       2.04609 (    8)
  covalent geometry    : bond        0.00458 ( 3823)
  covalent geometry    : angle       0.88242 ( 5183)

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

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

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  892 Ramachandran restraints generated.
    446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8334 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  194 LYS cc_start: 0.6825 (mmmt) cc_final: 0.6058 (mttp)
REVERT: A  204 GLN cc_start: 0.8689 (tt0) cc_final: 0.8386 (tp40)
REVERT: A  236 GLN cc_start: 0.7342 (tm-30) cc_final: 0.5945 (tt0)
REVERT: B  103 SER cc_start: 0.8455 (m) cc_final: 0.8231 (m)
REVERT: B  148 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6030 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 143
  average time/residue: 0.1347
  time to fit residues: 24.6727
Evaluate side-chains
  145 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  198 CYS
Chi-restraints excluded: chain A residue  215 PHE
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   32 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.168501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.141862 restraints weight = 7564.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.145522 restraints weight = 4594.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.148138 restraints weight = 3269.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.7385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   3836  Z= 0.179
  Angle     :  0.902  13.541   5218  Z= 0.430
  Chirality :  0.048   0.307    638
  Planarity :  0.003   0.027    615
  Dihedral  :  6.984  54.041    677
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  6.28 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 33.17 %
    Favored  : 63.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.79 (0.39), residues: 446
  helix:  1.99 (0.31), residues: 226
  sheet: -0.31 (0.64), residues: 63
  loop : -1.34 (0.52), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 202 
 HIS   0.002   0.001   HIS A  65 
 PHE   0.049   0.002   PHE A 127 
 TYR   0.019   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00919 (    5)
  link_NAG-ASN         : angle       4.88075 (   15)
  link_BETA1-4         : bond        0.00749 (    4)
  link_BETA1-4         : angle       3.04967 (   12)
  hydrogen bonds       : bond        0.04600 (  251)
  hydrogen bonds       : angle       4.42866 (  732)
  SS BOND              : bond        0.00704 (    4)
  SS BOND              : angle       1.93953 (    8)
  covalent geometry    : bond        0.00409 ( 3823)
  covalent geometry    : angle       0.84992 ( 5183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1620.67 seconds
wall clock time: 28 minutes 47.88 seconds (1727.88 seconds total)