Starting phenix.real_space_refine
on Fri May  9 20:45:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yrj_39543/05_2025/8yrj_39543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yrj_39543/05_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_39543/05_2025/8yrj_39543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yrj_39543/05_2025/8yrj_39543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yrj_39543/05_2025/8yrj_39543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yrj_39543/05_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-5687/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: 3.20, per 1000 atoms: 0.85
  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: 0.99
  Conformation dependent library (CDL) restraints added in 439.6 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: 0.36
  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: 1.14 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:             1.130
  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:                     13.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.720
-------------------------------------------------------------------------------
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  : 0.406 
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: 0.1630
  time to fit residues: 37.5203
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  : 0.422 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.160946 restraints weight = 4726.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.163654 restraints weight = 3305.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
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  : 0.432 
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: 0.8170 (p90) cc_final: 0.7769 (p90)
REVERT: A  137 TRP cc_start: 0.7137 (m-10) cc_final: 0.6620 (m-10)
REVERT: A  144 TYR cc_start: 0.7100 (m-80) cc_final: 0.6761 (m-10)
REVERT: A  222 LEU cc_start: 0.8701 (tt) cc_final: 0.8125 (tp)
REVERT: H   33 PHE cc_start: 0.8825 (t80) cc_final: 0.8388 (t80)
REVERT: H   37 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8582 (mm)
REVERT: B   51 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8080 (mm-30)
REVERT: B   79 ASP cc_start: 0.8414 (m-30) cc_final: 0.8167 (p0)
  outliers start: 18
  outliers final: 11
  residues processed: 141
  average time/residue: 0.1440
  time to fit residues: 25.1203
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  : 0.405 
-------------------------------------------------------------------------------
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:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.4282 r_free = 0.4282 target = 0.176034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151031 restraints weight = 7671.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.154933 restraints weight = 4685.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.157589 restraints weight = 3288.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3836  Z= 0.164
  Angle     :  0.861  14.519   5218  Z= 0.394
  Chirality :  0.047   0.216    638
  Planarity :  0.003   0.032    615
  Dihedral  : 10.776  58.262    677
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.93 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.70 %
    Favored  : 74.06 %
  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:  1.53 (0.40), residues: 446
  helix:  2.47 (0.32), residues: 235
  sheet:  0.59 (0.65), residues: 67
  loop : -1.34 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  42 
 HIS   0.006   0.001   HIS A  65 
 PHE   0.012   0.002   PHE B  45 
 TYR   0.028   0.002   TYR H  26 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01145 (    5)
  link_NAG-ASN         : angle       6.22112 (   15)
  link_BETA1-4         : bond        0.00937 (    4)
  link_BETA1-4         : angle       3.45511 (   12)
  hydrogen bonds       : bond        0.04244 (  251)
  hydrogen bonds       : angle       3.84753 (  732)
  SS BOND              : bond        0.01013 (    4)
  SS BOND              : angle       2.37526 (    8)
  covalent geometry    : bond        0.00338 ( 3823)
  covalent geometry    : angle       0.77302 ( 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
  146 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.7674 (tt0) cc_final: 0.7041 (tm-30)
REVERT: A  127 PHE cc_start: 0.8354 (p90) cc_final: 0.7982 (p90)
REVERT: A  144 TYR cc_start: 0.7054 (m-80) cc_final: 0.6692 (m-10)
REVERT: H   33 PHE cc_start: 0.8689 (t80) cc_final: 0.8438 (t80)
REVERT: B   79 ASP cc_start: 0.8452 (m-30) cc_final: 0.8233 (p0)
  outliers start: 17
  outliers final: 11
  residues processed: 138
  average time/residue: 0.1276
  time to fit residues: 22.1724
Evaluate side-chains
  131 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  141 ILE
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:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4310 r_free = 0.4310 target = 0.177975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.152119 restraints weight = 7566.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.155882 restraints weight = 4619.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.158351 restraints weight = 3263.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.4863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3836  Z= 0.166
  Angle     :  0.827  13.714   5218  Z= 0.378
  Chirality :  0.047   0.235    638
  Planarity :  0.003   0.030    615
  Dihedral  :  8.049  58.121    677
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.69 %
    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:  1.32 (0.40), residues: 446
  helix:  2.45 (0.32), residues: 234
  sheet:  0.06 (0.72), residues: 55
  loop : -1.34 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   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        0.01155 (    5)
  link_NAG-ASN         : angle       5.93679 (   15)
  link_BETA1-4         : bond        0.01006 (    4)
  link_BETA1-4         : angle       3.88781 (   12)
  hydrogen bonds       : bond        0.04279 (  251)
  hydrogen bonds       : angle       3.89756 (  732)
  SS BOND              : bond        0.00679 (    4)
  SS BOND              : angle       1.87767 (    8)
  covalent geometry    : bond        0.00355 ( 3823)
  covalent geometry    : angle       0.73913 ( 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: 15
    poor density    : 136
  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  127 PHE cc_start: 0.8332 (p90) cc_final: 0.7995 (p90)
REVERT: A  144 TYR cc_start: 0.6971 (m-80) cc_final: 0.6642 (m-10)
REVERT: H   33 PHE cc_start: 0.8622 (t80) cc_final: 0.7589 (t80)
REVERT: B  103 SER cc_start: 0.7989 (m) cc_final: 0.7688 (m)
  outliers start: 15
  outliers final: 14
  residues processed: 143
  average time/residue: 0.1331
  time to fit residues: 24.1220
Evaluate side-chains
  143 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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  167 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0970
   chunk 2 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4293 r_free = 0.4293 target = 0.177240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.151708 restraints weight = 7580.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.155643 restraints weight = 4409.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.158310 restraints weight = 3012.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.5350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3836  Z= 0.156
  Angle     :  0.820  13.724   5218  Z= 0.383
  Chirality :  0.046   0.229    638
  Planarity :  0.003   0.033    615
  Dihedral  :  7.130  56.963    677
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.44 %
    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:  1.58 (0.40), residues: 446
  helix:  2.60 (0.32), residues: 224
  sheet:  0.33 (0.72), residues: 55
  loop : -0.91 (0.51), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 137 
 HIS   0.002   0.001   HIS A  65 
 PHE   0.024   0.002   PHE H  33 
 TYR   0.012   0.001   TYR B 193 
 ARG   0.001   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01159 (    5)
  link_NAG-ASN         : angle       5.85351 (   15)
  link_BETA1-4         : bond        0.00687 (    4)
  link_BETA1-4         : angle       3.57833 (   12)
  hydrogen bonds       : bond        0.04393 (  251)
  hydrogen bonds       : angle       3.81464 (  732)
  SS BOND              : bond        0.00684 (    4)
  SS BOND              : angle       2.11549 (    8)
  covalent geometry    : bond        0.00325 ( 3823)
  covalent geometry    : angle       0.73578 ( 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
  150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.402 
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: 0.8377 (p90) cc_final: 0.8060 (p90)
REVERT: A  144 TYR cc_start: 0.7001 (m-80) cc_final: 0.6551 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1349
  time to fit residues: 24.0329
Evaluate side-chains
  141 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.175642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.149236 restraints weight = 7417.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.153293 restraints weight = 4339.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.155954 restraints weight = 2976.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3836  Z= 0.168
  Angle     :  0.834  13.380   5218  Z= 0.391
  Chirality :  0.047   0.216    638
  Planarity :  0.003   0.031    615
  Dihedral  :  6.735  56.438    677
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.71 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.18 %
    Favored  : 68.83 %
  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:  1.51 (0.40), residues: 446
  helix:  2.49 (0.31), residues: 222
  sheet:  0.45 (0.72), residues: 55
  loop : -0.89 (0.52), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 137 
 HIS   0.002   0.001   HIS A  65 
 PHE   0.009   0.001   PHE A 215 
 TYR   0.020   0.002   TYR B 193 
 ARG   0.002   0.000   ARG A 162 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01054 (    5)
  link_NAG-ASN         : angle       5.74533 (   15)
  link_BETA1-4         : bond        0.00743 (    4)
  link_BETA1-4         : angle       3.41103 (   12)
  hydrogen bonds       : bond        0.04365 (  251)
  hydrogen bonds       : angle       3.90782 (  732)
  SS BOND              : bond        0.00677 (    4)
  SS BOND              : angle       1.75556 (    8)
  covalent geometry    : bond        0.00356 ( 3823)
  covalent geometry    : angle       0.75751 ( 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
  148 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8316 (p90) cc_final: 0.8035 (p90)
REVERT: A  135 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7998 (ttpt)
REVERT: A  203 LEU cc_start: 0.9582 (mt) cc_final: 0.9353 (mt)
REVERT: A  204 GLN cc_start: 0.8408 (tt0) cc_final: 0.7895 (tp40)
REVERT: A  218 ASP cc_start: 0.7182 (t0) cc_final: 0.6803 (t0)
REVERT: B  103 SER cc_start: 0.8088 (m) cc_final: 0.7836 (m)
REVERT: B  148 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.5962 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 141
  average time/residue: 0.1358
  time to fit residues: 24.1743
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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 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:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.172782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.146168 restraints weight = 7590.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.149905 restraints weight = 4611.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.152530 restraints weight = 3265.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.5981

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= 0.167
  Angle     :  0.827  12.855   5218  Z= 0.386
  Chirality :  0.047   0.271    638
  Planarity :  0.003   0.033    615
  Dihedral  :  6.633  56.035    677
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 28.18 %
    Favored  : 67.08 %
  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:  1.32 (0.40), residues: 446
  helix:  2.33 (0.32), residues: 222
  sheet:  0.31 (0.70), residues: 56
  loop : -0.96 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 202 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.016   0.002   PHE H  33 
 TYR   0.016   0.002   TYR A 144 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01024 (    5)
  link_NAG-ASN         : angle       5.61464 (   15)
  link_BETA1-4         : bond        0.00723 (    4)
  link_BETA1-4         : angle       3.31508 (   12)
  hydrogen bonds       : bond        0.04475 (  251)
  hydrogen bonds       : angle       4.02543 (  732)
  SS BOND              : bond        0.00787 (    4)
  SS BOND              : angle       1.86099 (    8)
  covalent geometry    : bond        0.00353 ( 3823)
  covalent geometry    : angle       0.75312 ( 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
  150 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.414 
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: 0.8335 (p90) cc_final: 0.8047 (p90)
REVERT: A  135 LYS cc_start: 0.8243 (ttpt) cc_final: 0.8011 (tptp)
REVERT: A  144 TYR cc_start: 0.6690 (m-80) cc_final: 0.6241 (m-10)
REVERT: A  204 GLN cc_start: 0.8421 (tt0) cc_final: 0.7920 (tp40)
REVERT: A  218 ASP cc_start: 0.7140 (t0) cc_final: 0.6906 (t0)
REVERT: H   52 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8569 (mmmt)
REVERT: B   51 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7799 (mt-10)
REVERT: B  103 SER cc_start: 0.8173 (m) cc_final: 0.7874 (m)
REVERT: B  148 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.5893 (t80)
  outliers start: 19
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1264
  time to fit residues: 22.7051
Evaluate side-chains
  147 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0050
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.4276 r_free = 0.4276 target = 0.174947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.148988 restraints weight = 7369.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.152822 restraints weight = 4396.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.155441 restraints weight = 3070.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.6133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3836  Z= 0.154
  Angle     :  0.815  12.459   5218  Z= 0.382
  Chirality :  0.047   0.282    638
  Planarity :  0.003   0.031    615
  Dihedral  :  6.553  55.716    677
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.48 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 28.43 %
    Favored  : 66.08 %
  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:  1.23 (0.40), residues: 446
  helix:  2.17 (0.32), residues: 226
  sheet:  0.49 (0.70), residues: 56
  loop : -1.03 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 202 
 HIS   0.002   0.000   HIS A  65 
 PHE   0.019   0.002   PHE H  33 
 TYR   0.013   0.001   TYR A 200 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01017 (    5)
  link_NAG-ASN         : angle       5.46734 (   15)
  link_BETA1-4         : bond        0.00764 (    4)
  link_BETA1-4         : angle       3.20673 (   12)
  hydrogen bonds       : bond        0.04509 (  251)
  hydrogen bonds       : angle       4.09503 (  732)
  SS BOND              : bond        0.00588 (    4)
  SS BOND              : angle       1.37953 (    8)
  covalent geometry    : bond        0.00321 ( 3823)
  covalent geometry    : angle       0.74578 ( 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
  151 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8263 (p90) cc_final: 0.8000 (p90)
REVERT: A  135 LYS cc_start: 0.8246 (ttpt) cc_final: 0.8000 (tptp)
REVERT: A  144 TYR cc_start: 0.6690 (m-80) cc_final: 0.6312 (m-10)
REVERT: A  204 GLN cc_start: 0.8411 (tt0) cc_final: 0.8047 (tp40)
REVERT: H   52 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8529 (mmmt)
REVERT: B   51 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7856 (mt-10)
REVERT: B  148 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.5961 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1243
  time to fit residues: 22.4253
Evaluate side-chains
  142 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.171572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.144914 restraints weight = 7438.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.148607 restraints weight = 4536.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.151253 restraints weight = 3211.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.6436

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= 0.182
  Angle     :  0.852  12.753   5218  Z= 0.401
  Chirality :  0.049   0.329    638
  Planarity :  0.003   0.030    615
  Dihedral  :  6.707  54.695    677
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.26 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 28.68 %
    Favored  : 66.08 %
  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:  1.08 (0.40), residues: 446
  helix:  2.07 (0.32), residues: 226
  sheet:  0.34 (0.69), residues: 56
  loop : -1.11 (0.51), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 202 
 HIS   0.002   0.001   HIS A  65 
 PHE   0.024   0.002   PHE H  33 
 TYR   0.027   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00949 (    5)
  link_NAG-ASN         : angle       5.38834 (   15)
  link_BETA1-4         : bond        0.00687 (    4)
  link_BETA1-4         : angle       3.12821 (   12)
  hydrogen bonds       : bond        0.04624 (  251)
  hydrogen bonds       : angle       4.12443 (  732)
  SS BOND              : bond        0.00615 (    4)
  SS BOND              : angle       2.65301 (    8)
  covalent geometry    : bond        0.00400 ( 3823)
  covalent geometry    : angle       0.78337 ( 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
  153 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8351 (p90) cc_final: 0.8040 (p90)
REVERT: A  135 LYS cc_start: 0.8260 (ttpt) cc_final: 0.8044 (tptp)
REVERT: A  144 TYR cc_start: 0.6808 (m-80) cc_final: 0.6428 (m-10)
REVERT: A  204 GLN cc_start: 0.8474 (tt0) cc_final: 0.8160 (tp40)
REVERT: B  103 SER cc_start: 0.8289 (m) cc_final: 0.8037 (m)
REVERT: B  148 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.5987 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1378
  time to fit residues: 25.2173
Evaluate side-chains
  148 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
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   61 THR
Chi-restraints excluded: chain A residue   70 SER
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0040
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1198

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.168314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.141511 restraints weight = 7737.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.145194 restraints weight = 4719.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.147657 restraints weight = 3364.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.6823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3836  Z= 0.197
  Angle     :  0.882  13.593   5218  Z= 0.420
  Chirality :  0.050   0.370    638
  Planarity :  0.003   0.028    615
  Dihedral  :  6.829  54.487    677
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  5.16 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 30.67 %
    Favored  : 64.59 %
  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:  0.82 (0.40), residues: 446
  helix:  1.88 (0.32), residues: 226
  sheet:  0.14 (0.69), residues: 56
  loop : -1.23 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  95 
 HIS   0.003   0.001   HIS A  65 
 PHE   0.025   0.002   PHE H  33 
 TYR   0.023   0.002   TYR B  92 
 ARG   0.003   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00870 (    5)
  link_NAG-ASN         : angle       5.24183 (   15)
  link_BETA1-4         : bond        0.00662 (    4)
  link_BETA1-4         : angle       3.07695 (   12)
  hydrogen bonds       : bond        0.04798 (  251)
  hydrogen bonds       : angle       4.21207 (  732)
  SS BOND              : bond        0.01103 (    4)
  SS BOND              : angle       2.20511 (    8)
  covalent geometry    : bond        0.00431 ( 3823)
  covalent geometry    : angle       0.82163 ( 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
  154 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8071 (m-10) cc_final: 0.7767 (m-10)
REVERT: A  127 PHE cc_start: 0.8387 (p90) cc_final: 0.8083 (p90)
REVERT: A  135 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8076 (tptp)
REVERT: A  144 TYR cc_start: 0.7026 (m-80) cc_final: 0.6610 (m-10)
REVERT: H   52 LYS cc_start: 0.9226 (mmtp) cc_final: 0.8615 (mmmt)
REVERT: B   51 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7904 (mt-10)
REVERT: B  103 SER cc_start: 0.8371 (m) cc_final: 0.8128 (m)
REVERT: B  148 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6060 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1234
  time to fit residues: 22.6218
Evaluate side-chains
  146 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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   61 THR
Chi-restraints excluded: chain A residue   70 SER
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 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   77 VAL
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:    0.0570
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.170826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.142860 restraints weight = 7565.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.146928 restraints weight = 4497.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.149660 restraints weight = 3147.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.6983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3836  Z= 0.165
  Angle     :  0.885  13.311   5218  Z= 0.416
  Chirality :  0.048   0.358    638
  Planarity :  0.003   0.027    615
  Dihedral  :  6.765  54.531    677
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 30.17 %
    Favored  : 65.09 %
  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:  0.88 (0.40), residues: 446
  helix:  1.90 (0.32), residues: 226
  sheet:  0.19 (0.69), residues: 56
  loop : -1.19 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  95 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.021   0.002   PHE H  33 
 TYR   0.018   0.002   TYR B  92 
 ARG   0.002   0.000   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00891 (    5)
  link_NAG-ASN         : angle       5.02190 (   15)
  link_BETA1-4         : bond        0.00757 (    4)
  link_BETA1-4         : angle       3.03533 (   12)
  hydrogen bonds       : bond        0.04611 (  251)
  hydrogen bonds       : angle       4.26209 (  732)
  SS BOND              : bond        0.00659 (    4)
  SS BOND              : angle       1.54721 (    8)
  covalent geometry    : bond        0.00355 ( 3823)
  covalent geometry    : angle       0.83109 ( 5183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1562.28 seconds
wall clock time: 28 minutes 1.88 seconds (1681.88 seconds total)