Starting phenix.real_space_refine
on Sun Apr 27 03:15:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpu_44790/04_2025/9bpu_44790.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2744      2.51       5
     N     743      2.21       5
     O     804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4318
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1068
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 10, 'TRANS': 127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1613
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "B"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1570
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 19, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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
  Time building chain proxies: 3.26, per 1000 atoms: 0.75
  Number of scatterers: 4318
  At special positions: 0
  Unit cell: (67.284, 96.12, 104.664, 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      27     16.00
     O     804      8.00
     N     743      7.00
     C    2744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  27 " - pdb=" SG  CYS C 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  62 " - pdb=" SG  CYS C 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 175 " - pdb=" SG  CYS B 197 " 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 D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG D   1 " - " ASN B   9 "
      " NAG E   1 " - " ASN B 122 "
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 462.1 milliseconds
  

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 12 sheets defined
      23.4% alpha, 41.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 4.146A  pdb=" N   HIS C  31 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG C  33 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 58
    Processing helix  chain 'C' and resid 74 through 99
      removed outlier: 3.565A  pdb=" N   SER C  99 " --> pdb=" O   GLY C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 127
    Processing helix  chain 'C' and resid 149 through 167
      removed outlier: 3.690A  pdb=" N   ARG C 153 " --> pdb=" O   SER C 149 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU C 162 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ARG C 163 " --> pdb=" O   PHE C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 176
    Processing helix  chain 'A' and resid 106 through 111
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'B' and resid 99 through 103
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32
      removed outlier: 4.297A  pdb=" N   VAL A  27 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   GLN A  39 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   MET A  29 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A  37 " --> pdb=" O   MET A  29 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER A  31 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LYS A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69
      removed outlier: 6.715A  pdb=" N   ALA A  54 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   MET A  67 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE A  52 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A  86 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69
      removed outlier: 6.715A  pdb=" N   ALA A  54 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   MET A  67 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE A  52 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   THR A  86 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 123
    Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 15
    Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 41
    Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 41
    Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114
      removed outlier: 3.594A  pdb=" N   ASN B 122 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 152
    Processing sheet with id=AB3, first strand: chain 'B' and resid 151 through 152

    222 hydrogen bonds defined for protein.
    576 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1328
        1.34 -     1.45: 732
        1.45 -     1.57: 2336
        1.57 -     1.69: 1
        1.69 -     1.81: 37
  Bond restraints: 4434
  Sorted by residual:
  bond pdb=" N   MET B 131 "
       pdb=" CA  MET B 131 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.48e+01
  bond pdb=" N   TYR B  39 "
       pdb=" CA  TYR B  39 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.23e-02 6.61e+03 8.83e+00
  bond pdb=" N   SER B 190 "
       pdb=" CA  SER B 190 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.09e-02 8.42e+03 8.60e+00
  bond pdb=" N   VAL A 122 "
       pdb=" CA  VAL A 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.20e-02 6.94e+03 8.14e+00
  bond pdb=" N   TYR B 125 "
       pdb=" CA  TYR B 125 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.23e-02 6.61e+03 7.99e+00
  ... (remaining 4429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 5733
        1.73 -     3.45: 251
        3.45 -     5.18: 39
        5.18 -     6.90: 7
        6.90 -     8.63: 2
  Bond angle restraints: 6032
  Sorted by residual:
  angle pdb=" C   ALA A 124 "
        pdb=" CA  ALA A 124 "
        pdb=" CB  ALA A 124 "
      ideal   model   delta    sigma   weight residual
     117.23  111.85    5.38 1.36e+00 5.41e-01 1.57e+01
  angle pdb=" CA  GLN B 126 "
        pdb=" C   GLN B 126 "
        pdb=" O   GLN B 126 "
      ideal   model   delta    sigma   weight residual
     122.51  118.14    4.37 1.34e+00 5.57e-01 1.06e+01
  angle pdb=" CA  ASP B  71 "
        pdb=" C   ASP B  71 "
        pdb=" O   ASP B  71 "
      ideal   model   delta    sigma   weight residual
     121.58  118.05    3.53 1.12e+00 7.97e-01 9.95e+00
  angle pdb=" CA  GLN B   8 "
        pdb=" C   GLN B   8 "
        pdb=" O   GLN B   8 "
      ideal   model   delta    sigma   weight residual
     120.70  117.54    3.16 1.03e+00 9.43e-01 9.43e+00
  angle pdb=" CA  GLY A  48 "
        pdb=" C   GLY A  48 "
        pdb=" O   GLY A  48 "
      ideal   model   delta    sigma   weight residual
     122.33  118.28    4.05 1.32e+00 5.74e-01 9.42e+00
  ... (remaining 6027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.12: 2479
       22.12 -    44.25: 233
       44.25 -    66.37: 45
       66.37 -    88.49: 9
       88.49 -   110.62: 6
  Dihedral angle restraints: 2772
    sinusoidal: 1210
      harmonic: 1562
  Sorted by residual:
  dihedral pdb=" CB  CYS C  62 "
           pdb=" SG  CYS C  62 "
           pdb=" SG  CYS C 152 "
           pdb=" CB  CYS C 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.02   31.98     1      1.00e+01 1.00e-02 1.46e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  178.09  110.62     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C3  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -61.13  108.75     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 2769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 530
       0.054 -    0.107: 101
       0.107 -    0.161: 31
       0.161 -    0.214: 5
       0.214 -    0.268: 2
  Chirality restraints: 669
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 122 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B   9 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 666 not shown)

  Planarity restraints: 775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  42 "    0.035 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A  43 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  50 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" CD  GLU B  50 "    0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  50 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  50 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 100 "   -0.016 2.00e-02 2.50e+03   8.96e-03 2.01e+00
        pdb=" CG  TRP A 100 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 100 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 100 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 100 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 100 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 100 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 772 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 523
        2.75 -     3.29: 4033
        3.29 -     3.83: 7185
        3.83 -     4.36: 8209
        4.36 -     4.90: 14499
  Nonbonded interactions: 34449
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 138 "
            pdb=" O   GLN B 160 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER B  84 "
            pdb=" O   SER B  87 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" OE1 GLU A  92 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NE2 GLN A 157 "
            pdb=" OE1 GLN A 190 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NH2 ARG C  47 "
            pdb=" OD2 ASP B  98 "
     model   vdw
     2.336 3.120
  ... (remaining 34444 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.320
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
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      :  0.006   0.087   4446  Z= 0.347
  Angle     :  0.781   8.626   6061  Z= 0.455
  Chirality :  0.051   0.268    669
  Planarity :  0.004   0.051    773
  Dihedral  : 17.752 110.615   1735
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 24.79 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.38), residues: 521
  helix:  1.86 (0.49), residues: 119
  sheet: -0.54 (0.36), residues: 203
  loop : -0.42 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 100 
 HIS   0.007   0.001   HIS A  97 
 PHE   0.007   0.001   PHE B 153 
 TYR   0.012   0.001   TYR B 125 
 ARG   0.005   0.000   ARG A  88 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00234 (    2)
  link_NAG-ASN         : angle       1.22201 (    6)
  link_BETA1-4         : bond        0.00291 (    3)
  link_BETA1-4         : angle       1.67583 (    9)
  hydrogen bonds       : bond        0.13976 (  180)
  hydrogen bonds       : angle       6.77233 (  576)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       0.59973 (   14)
  covalent geometry    : bond        0.00551 ( 4434)
  covalent geometry    : angle       0.77914 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.8178 (mt) cc_final: 0.7926 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 98
  average time/residue: 0.1629
  time to fit residues: 20.0407
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue  134 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0170
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.9422

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

Flipped N/Q/H residues before XYZ refinement:
A 168 GLN
B 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.175722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.147269 restraints weight = 5379.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.40
r_work: 0.3648 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4446  Z= 0.151
  Angle     :  0.610   7.111   6061  Z= 0.298
  Chirality :  0.042   0.136    669
  Planarity :  0.004   0.034    773
  Dihedral  :  9.331  63.099    690
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.58 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.37), residues: 521
  helix:  1.86 (0.49), residues: 119
  sheet: -0.47 (0.36), residues: 202
  loop : -0.27 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.018   0.001   PHE A  62 
 TYR   0.015   0.001   TYR B 138 
 ARG   0.004   0.000   ARG A  88 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    2)
  link_NAG-ASN         : angle       0.81566 (    6)
  link_BETA1-4         : bond        0.00350 (    3)
  link_BETA1-4         : angle       2.42751 (    9)
  hydrogen bonds       : bond        0.03462 (  180)
  hydrogen bonds       : angle       4.89812 (  576)
  SS BOND              : bond        0.00251 (    7)
  SS BOND              : angle       0.63177 (   14)
  covalent geometry    : bond        0.00359 ( 4434)
  covalent geometry    : angle       0.60335 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8443 (t0) cc_final: 0.8191 (t0)
REVERT: A   88 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8196 (ttp-170)
REVERT: B   40 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7409 (tt0)
REVERT: B  117 GLU cc_start: 0.7295 (pt0) cc_final: 0.7091 (pt0)
  outliers start: 22
  outliers final: 12
  residues processed: 97
  average time/residue: 0.2019
  time to fit residues: 24.7863
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.175382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.147141 restraints weight = 5335.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.39
r_work: 0.3650 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3499 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4446  Z= 0.129
  Angle     :  0.579   7.164   6061  Z= 0.280
  Chirality :  0.041   0.133    669
  Planarity :  0.004   0.030    773
  Dihedral  :  7.786  55.908    690
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.15 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.38), residues: 521
  helix:  2.53 (0.48), residues: 111
  sheet: -0.42 (0.36), residues: 201
  loop : -0.25 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.010   0.001   PHE A  62 
 TYR   0.011   0.001   TYR B 138 
 ARG   0.002   0.000   ARG A  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    2)
  link_NAG-ASN         : angle       0.68791 (    6)
  link_BETA1-4         : bond        0.00400 (    3)
  link_BETA1-4         : angle       2.23343 (    9)
  hydrogen bonds       : bond        0.03167 (  180)
  hydrogen bonds       : angle       4.67140 (  576)
  SS BOND              : bond        0.00206 (    7)
  SS BOND              : angle       0.53365 (   14)
  covalent geometry    : bond        0.00304 ( 4434)
  covalent geometry    : angle       0.57306 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8469 (t0) cc_final: 0.7967 (t0)
REVERT: A   88 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8005 (ttp-170)
REVERT: B   40 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7344 (tt0)
REVERT: B  117 GLU cc_start: 0.7202 (pt0) cc_final: 0.6856 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 89
  average time/residue: 0.1619
  time to fit residues: 18.3957
Evaluate side-chains
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.169740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.140852 restraints weight = 5423.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.43
r_work: 0.3571 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4446  Z= 0.242
  Angle     :  0.660   6.869   6061  Z= 0.325
  Chirality :  0.043   0.138    669
  Planarity :  0.004   0.032    773
  Dihedral  :  7.415  56.424    690
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 18.38 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.37), residues: 521
  helix:  2.16 (0.47), residues: 111
  sheet: -0.67 (0.36), residues: 201
  loop : -0.35 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 152 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.014   0.002   PHE A  62 
 TYR   0.016   0.002   TYR B  99 
 ARG   0.003   0.001   ARG C  33 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00687 (    2)
  link_NAG-ASN         : angle       1.14028 (    6)
  link_BETA1-4         : bond        0.00327 (    3)
  link_BETA1-4         : angle       2.05646 (    9)
  hydrogen bonds       : bond        0.03818 (  180)
  hydrogen bonds       : angle       5.00256 (  576)
  SS BOND              : bond        0.00429 (    7)
  SS BOND              : angle       0.87633 (   14)
  covalent geometry    : bond        0.00572 ( 4434)
  covalent geometry    : angle       0.65466 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8540 (t0) cc_final: 0.7976 (t0)
REVERT: B   40 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7576 (tt0)
REVERT: B   59 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6353 (pt0)
REVERT: B  117 GLU cc_start: 0.7210 (pt0) cc_final: 0.6731 (pt0)
  outliers start: 26
  outliers final: 19
  residues processed: 104
  average time/residue: 0.1580
  time to fit residues: 20.9858
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  122 CYS
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.173374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.144598 restraints weight = 5464.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.44
r_work: 0.3624 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4446  Z= 0.132
  Angle     :  0.586   7.591   6061  Z= 0.286
  Chirality :  0.041   0.137    669
  Planarity :  0.004   0.031    773
  Dihedral  :  7.007  55.488    690
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.23 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.38), residues: 521
  helix:  2.39 (0.48), residues: 111
  sheet: -0.55 (0.37), residues: 201
  loop : -0.33 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.008   0.001   PHE B 153 
 TYR   0.011   0.001   TYR B 138 
 ARG   0.003   0.000   ARG A  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    2)
  link_NAG-ASN         : angle       0.62728 (    6)
  link_BETA1-4         : bond        0.00368 (    3)
  link_BETA1-4         : angle       1.67361 (    9)
  hydrogen bonds       : bond        0.03072 (  180)
  hydrogen bonds       : angle       4.66882 (  576)
  SS BOND              : bond        0.00181 (    7)
  SS BOND              : angle       0.80832 (   14)
  covalent geometry    : bond        0.00311 ( 4434)
  covalent geometry    : angle       0.58172 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8332 (t0) cc_final: 0.7851 (t0)
REVERT: B   59 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6131 (pt0)
REVERT: B  117 GLU cc_start: 0.6991 (pt0) cc_final: 0.6593 (pt0)
  outliers start: 22
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1646
  time to fit residues: 21.0066
Evaluate side-chains
  91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0470
   overall best weight:    0.5078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.175623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.147131 restraints weight = 5392.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.42
r_work: 0.3658 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4446  Z= 0.110
  Angle     :  0.573   7.732   6061  Z= 0.277
  Chirality :  0.040   0.148    669
  Planarity :  0.004   0.036    773
  Dihedral  :  6.793  54.882    690
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.23 %
    Favored  : 76.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.38), residues: 521
  helix:  2.57 (0.47), residues: 116
  sheet: -0.44 (0.37), residues: 194
  loop : -0.25 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.006   0.001   PHE B 142 
 TYR   0.011   0.001   TYR B 138 
 ARG   0.002   0.000   ARG C  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    2)
  link_NAG-ASN         : angle       0.68928 (    6)
  link_BETA1-4         : bond        0.00356 (    3)
  link_BETA1-4         : angle       1.55519 (    9)
  hydrogen bonds       : bond        0.02817 (  180)
  hydrogen bonds       : angle       4.44594 (  576)
  SS BOND              : bond        0.00248 (    7)
  SS BOND              : angle       0.86338 (   14)
  covalent geometry    : bond        0.00258 ( 4434)
  covalent geometry    : angle       0.56939 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8460 (t0) cc_final: 0.8027 (t0)
REVERT: A   88 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.7870 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6223 (pt0)
REVERT: B   68 LYS cc_start: 0.8305 (tppt) cc_final: 0.7957 (tppp)
REVERT: B  117 GLU cc_start: 0.7260 (pt0) cc_final: 0.6846 (pt0)
  outliers start: 22
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1665
  time to fit residues: 20.1128
Evaluate side-chains
  100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   88 LYS
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 4 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3936

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.176601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.148474 restraints weight = 5368.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.41
r_work: 0.3676 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4446  Z= 0.104
  Angle     :  0.572   8.054   6061  Z= 0.277
  Chirality :  0.040   0.154    669
  Planarity :  0.004   0.031    773
  Dihedral  :  6.657  54.574    690
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.15 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.38), residues: 521
  helix:  2.66 (0.47), residues: 116
  sheet: -0.37 (0.37), residues: 194
  loop : -0.27 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 100 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.006   0.001   PHE B 142 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    2)
  link_NAG-ASN         : angle       0.61955 (    6)
  link_BETA1-4         : bond        0.00353 (    3)
  link_BETA1-4         : angle       1.45610 (    9)
  hydrogen bonds       : bond        0.02676 (  180)
  hydrogen bonds       : angle       4.30035 (  576)
  SS BOND              : bond        0.00265 (    7)
  SS BOND              : angle       0.80880 (   14)
  covalent geometry    : bond        0.00243 ( 4434)
  covalent geometry    : angle       0.56914 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8274 (t0) cc_final: 0.7841 (t0)
REVERT: B   59 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6067 (pt0)
REVERT: B   68 LYS cc_start: 0.8125 (tppt) cc_final: 0.7835 (tppp)
REVERT: B  117 GLU cc_start: 0.7036 (pt0) cc_final: 0.6651 (pt0)
  outliers start: 15
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1760
  time to fit residues: 20.3420
Evaluate side-chains
  84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 41 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0370
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.175699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.147984 restraints weight = 5349.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.36
r_work: 0.3666 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4446  Z= 0.118
  Angle     :  0.580   8.083   6061  Z= 0.280
  Chirality :  0.040   0.152    669
  Planarity :  0.004   0.031    773
  Dihedral  :  6.656  54.756    690
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.86 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.38), residues: 521
  helix:  2.61 (0.46), residues: 116
  sheet: -0.37 (0.38), residues: 194
  loop : -0.25 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 100 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.007   0.001   PHE B 101 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.005   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    2)
  link_NAG-ASN         : angle       0.72488 (    6)
  link_BETA1-4         : bond        0.00365 (    3)
  link_BETA1-4         : angle       1.46160 (    9)
  hydrogen bonds       : bond        0.02739 (  180)
  hydrogen bonds       : angle       4.27761 (  576)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       0.66631 (   14)
  covalent geometry    : bond        0.00276 ( 4434)
  covalent geometry    : angle       0.57714 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8455 (t0) cc_final: 0.8038 (t0)
REVERT: B   59 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6199 (pt0)
REVERT: B   68 LYS cc_start: 0.8186 (tppt) cc_final: 0.7886 (tppp)
REVERT: B  117 GLU cc_start: 0.7267 (pt0) cc_final: 0.6779 (pt0)
  outliers start: 12
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1805
  time to fit residues: 19.4869
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0270
   chunk 15 optimal weight:    0.0970
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.2474

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.179287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152043 restraints weight = 5403.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 2.36
r_work: 0.3707 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4446  Z= 0.093
  Angle     :  0.566   8.415   6061  Z= 0.272
  Chirality :  0.040   0.161    669
  Planarity :  0.004   0.041    773
  Dihedral  :  6.525  54.124    690
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 22.86 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.38), residues: 521
  helix:  2.78 (0.47), residues: 116
  sheet: -0.27 (0.38), residues: 194
  loop : -0.23 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 100 
 HIS   0.007   0.001   HIS A  97 
 PHE   0.007   0.001   PHE B 142 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.004   0.000   ARG A  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00104 (    2)
  link_NAG-ASN         : angle       0.64010 (    6)
  link_BETA1-4         : bond        0.00345 (    3)
  link_BETA1-4         : angle       1.34335 (    9)
  hydrogen bonds       : bond        0.02458 (  180)
  hydrogen bonds       : angle       4.09304 (  576)
  SS BOND              : bond        0.00199 (    7)
  SS BOND              : angle       0.60829 (   14)
  covalent geometry    : bond        0.00217 ( 4434)
  covalent geometry    : angle       0.56426 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8407 (t0) cc_final: 0.8008 (t0)
REVERT: A   88 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7822 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6120 (pt0)
REVERT: B   68 LYS cc_start: 0.8162 (tppt) cc_final: 0.7862 (tppp)
REVERT: B  117 GLU cc_start: 0.7240 (pt0) cc_final: 0.6760 (pt0)
  outliers start: 11
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1750
  time to fit residues: 19.4070
Evaluate side-chains
  85 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   40 GLN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 42 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 173 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.176393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.148414 restraints weight = 5291.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.38
r_work: 0.3671 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4446  Z= 0.119
  Angle     :  0.578   8.360   6061  Z= 0.279
  Chirality :  0.040   0.154    669
  Planarity :  0.004   0.038    773
  Dihedral  :  6.597  54.758    690
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.29 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.38), residues: 521
  helix:  2.34 (0.47), residues: 122
  sheet: -0.30 (0.38), residues: 194
  loop : -0.08 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 152 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.006   0.001   PHE B 153 
 TYR   0.009   0.001   TYR B 138 
 ARG   0.004   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00254 (    2)
  link_NAG-ASN         : angle       0.77303 (    6)
  link_BETA1-4         : bond        0.00349 (    3)
  link_BETA1-4         : angle       1.42198 (    9)
  hydrogen bonds       : bond        0.02658 (  180)
  hydrogen bonds       : angle       4.17667 (  576)
  SS BOND              : bond        0.00267 (    7)
  SS BOND              : angle       0.57332 (   14)
  covalent geometry    : bond        0.00281 ( 4434)
  covalent geometry    : angle       0.57511 ( 6032)

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

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

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1042 Ramachandran restraints generated.
    521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8453 (t0) cc_final: 0.8053 (t0)
REVERT: A   88 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.7993 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6165 (pt0)
REVERT: B   68 LYS cc_start: 0.8144 (tppt) cc_final: 0.7862 (tppp)
REVERT: B  117 GLU cc_start: 0.7243 (pt0) cc_final: 0.6801 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1674
  time to fit residues: 17.6628
Evaluate side-chains
  93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   18 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0370
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN
B 173 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.175664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.147398 restraints weight = 5374.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.41
r_work: 0.3657 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4446  Z= 0.128
  Angle     :  0.592   8.328   6061  Z= 0.287
  Chirality :  0.040   0.151    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.634  54.848    690
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.93 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.38), residues: 521
  helix:  2.34 (0.47), residues: 122
  sheet: -0.48 (0.37), residues: 204
  loop :  0.07 (0.47), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 100 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.007   0.001   PHE B 153 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.004   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00242 (    2)
  link_NAG-ASN         : angle       0.73829 (    6)
  link_BETA1-4         : bond        0.00354 (    3)
  link_BETA1-4         : angle       1.39952 (    9)
  hydrogen bonds       : bond        0.02735 (  180)
  hydrogen bonds       : angle       4.25063 (  576)
  SS BOND              : bond        0.00260 (    7)
  SS BOND              : angle       0.57729 (   14)
  covalent geometry    : bond        0.00300 ( 4434)
  covalent geometry    : angle       0.58951 ( 6032)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2784.40 seconds
wall clock time: 48 minutes 33.88 seconds (2913.88 seconds total)