Starting phenix.real_space_refine
on Sat May 10 00:07:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpu_44790/05_2025/9bpu_44790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpu_44790/05_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_44790/05_2025/9bpu_44790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpu_44790/05_2025/9bpu_44790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpu_44790/05_2025/9bpu_44790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpu_44790/05_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-5687/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: 3.17, per 1000 atoms: 0.73
  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: 1.20
  Conformation dependent library (CDL) restraints added in 514.7 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: 0.59
  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: 1.16

  Time building geometry restraints manager: 1.40 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:             0.510
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.850
  Find NCS groups from input model:        0.050
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
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  : 0.494 
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: 0.1679
  time to fit residues: 20.6355
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  : 0.498 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.174324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.145536 restraints weight = 5392.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.43
r_work: 0.3640 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4446  Z= 0.168
  Angle     :  0.619   7.057   6061  Z= 0.303
  Chirality :  0.042   0.145    669
  Planarity :  0.004   0.033    773
  Dihedral  :  9.526  65.347    690
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 21.58 %
    Favored  : 73.93 %
  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:  1.95 (0.48), residues: 117
  sheet: -0.45 (0.36), residues: 201
  loop : -0.33 (0.44), residues: 203

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   0.017   0.002   PHE A  62 
 TYR   0.015   0.001   TYR B 138 
 ARG   0.003   0.000   ARG A  88 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00387 (    2)
  link_NAG-ASN         : angle       0.82879 (    6)
  link_BETA1-4         : bond        0.00484 (    3)
  link_BETA1-4         : angle       2.37371 (    9)
  hydrogen bonds       : bond        0.03754 (  180)
  hydrogen bonds       : angle       4.98664 (  576)
  SS BOND              : bond        0.00269 (    7)
  SS BOND              : angle       0.68979 (   14)
  covalent geometry    : bond        0.00399 ( 4434)
  covalent geometry    : angle       0.61269 ( 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
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8444 (t0) cc_final: 0.8203 (t0)
REVERT: B   40 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7414 (tt0)
  outliers start: 21
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1667
  time to fit residues: 20.5211
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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  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:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.173280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.144779 restraints weight = 5341.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.40
r_work: 0.3622 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4446  Z= 0.159
  Angle     :  0.599   7.099   6061  Z= 0.291
  Chirality :  0.042   0.134    669
  Planarity :  0.004   0.031    773
  Dihedral  :  7.710  56.202    690
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 19.23 %
    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:  0.22 (0.38), residues: 521
  helix:  2.34 (0.48), residues: 111
  sheet: -0.48 (0.36), residues: 201
  loop : -0.27 (0.44), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 152 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.012   0.001   PHE A  62 
 TYR   0.012   0.001   TYR B  99 
 ARG   0.003   0.000   ARG A  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00378 (    2)
  link_NAG-ASN         : angle       0.82679 (    6)
  link_BETA1-4         : bond        0.00395 (    3)
  link_BETA1-4         : angle       2.19523 (    9)
  hydrogen bonds       : bond        0.03434 (  180)
  hydrogen bonds       : angle       4.77268 (  576)
  SS BOND              : bond        0.00223 (    7)
  SS BOND              : angle       0.66938 (   14)
  covalent geometry    : bond        0.00377 ( 4434)
  covalent geometry    : angle       0.59345 ( 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
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  118 ASP cc_start: 0.7396 (m-30) cc_final: 0.7173 (m-30)
REVERT: A   26 ASN cc_start: 0.8511 (t0) cc_final: 0.8001 (t0)
REVERT: A   88 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.7968 (ttp-170)
REVERT: B   40 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7421 (tt0)
  outliers start: 24
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1733
  time to fit residues: 20.3335
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
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 A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 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  113 THR
Chi-restraints excluded: chain B residue  130 CYS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0170
   chunk 11 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.4098 r_free = 0.4098 target = 0.176295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.148332 restraints weight = 5370.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 2.39
r_work: 0.3670 rms_B_bonded: 2.92 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: 0.7610
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4446  Z= 0.106
  Angle     :  0.554   7.508   6061  Z= 0.268
  Chirality :  0.040   0.145    669
  Planarity :  0.003   0.031    773
  Dihedral  :  6.924  54.928    690
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.87 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.38), residues: 521
  helix:  2.66 (0.48), residues: 111
  sheet: -0.46 (0.37), residues: 194
  loop : -0.23 (0.43), residues: 216

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   0.007   0.001   PHE B 101 
 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        0.00187 (    2)
  link_NAG-ASN         : angle       0.53909 (    6)
  link_BETA1-4         : bond        0.00367 (    3)
  link_BETA1-4         : angle       1.91481 (    9)
  hydrogen bonds       : bond        0.02862 (  180)
  hydrogen bonds       : angle       4.47978 (  576)
  SS BOND              : bond        0.00218 (    7)
  SS BOND              : angle       0.48079 (   14)
  covalent geometry    : bond        0.00247 ( 4434)
  covalent geometry    : angle       0.54974 ( 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
  97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8492 (t0) cc_final: 0.8028 (t0)
REVERT: A   88 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.7982 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6098 (pt0)
  outliers start: 20
  outliers final: 12
  residues processed: 90
  average time/residue: 0.1461
  time to fit residues: 16.8878
Evaluate side-chains
  81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 TRP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 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  113 THR
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  191 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0370
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** B 167 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.175310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.148943 restraints weight = 5472.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.19
r_work: 0.3653 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1561

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= 0.116
  Angle     :  0.565   7.628   6061  Z= 0.273
  Chirality :  0.040   0.145    669
  Planarity :  0.003   0.032    773
  Dihedral  :  6.811  55.022    690
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.95 %
    Favored  : 76.50 %
  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:  0.41 (0.38), residues: 521
  helix:  2.61 (0.47), residues: 116
  sheet: -0.46 (0.37), residues: 194
  loop : -0.22 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 152 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.006   0.001   PHE B 142 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.003   0.000   ARG A  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    2)
  link_NAG-ASN         : angle       0.66662 (    6)
  link_BETA1-4         : bond        0.00351 (    3)
  link_BETA1-4         : angle       1.72362 (    9)
  hydrogen bonds       : bond        0.02869 (  180)
  hydrogen bonds       : angle       4.44074 (  576)
  SS BOND              : bond        0.00379 (    7)
  SS BOND              : angle       0.92560 (   14)
  covalent geometry    : bond        0.00274 ( 4434)
  covalent geometry    : angle       0.56070 ( 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
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8427 (t0) cc_final: 0.7989 (t0)
REVERT: A   88 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.7967 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6164 (pt0)
  outliers start: 26
  outliers final: 17
  residues processed: 92
  average time/residue: 0.1538
  time to fit residues: 17.9747
Evaluate side-chains
  90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
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  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  122 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  113 THR
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  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:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.167607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141360 restraints weight = 5439.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.09
r_work: 0.3552 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   4446  Z= 0.298
  Angle     :  0.724   7.103   6061  Z= 0.355
  Chirality :  0.045   0.137    669
  Planarity :  0.004   0.030    773
  Dihedral  :  7.408  56.641    690
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 17.74 %
    Favored  : 76.92 %
  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: -0.31 (0.37), residues: 521
  helix:  1.47 (0.47), residues: 117
  sheet: -0.77 (0.36), residues: 201
  loop : -0.41 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 152 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.016   0.002   PHE B 153 
 TYR   0.016   0.002   TYR B  99 
 ARG   0.004   0.001   ARG A 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00801 (    2)
  link_NAG-ASN         : angle       1.33202 (    6)
  link_BETA1-4         : bond        0.00337 (    3)
  link_BETA1-4         : angle       1.85065 (    9)
  hydrogen bonds       : bond        0.04105 (  180)
  hydrogen bonds       : angle       5.06548 (  576)
  SS BOND              : bond        0.00615 (    7)
  SS BOND              : angle       1.12669 (   14)
  covalent geometry    : bond        0.00706 ( 4434)
  covalent geometry    : angle       0.71920 ( 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
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8497 (t0) cc_final: 0.8010 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 100
  average time/residue: 0.1749
  time to fit residues: 21.7561
Evaluate side-chains
  100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  102 LEU
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain A residue   47 LYS
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   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=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:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.4059 r_free = 0.4059 target = 0.173868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.147189 restraints weight = 5359.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.19
r_work: 0.3642 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4446  Z= 0.111
  Angle     :  0.594   8.011   6061  Z= 0.287
  Chirality :  0.042   0.307    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.869  54.862    690
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 20.51 %
    Favored  : 75.21 %
  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:  0.15 (0.38), residues: 521
  helix:  2.05 (0.48), residues: 122
  sheet: -0.53 (0.37), residues: 194
  loop : -0.31 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 100 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.009   0.001   PHE B 142 
 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        0.00107 (    2)
  link_NAG-ASN         : angle       0.55408 (    6)
  link_BETA1-4         : bond        0.00355 (    3)
  link_BETA1-4         : angle       1.47097 (    9)
  hydrogen bonds       : bond        0.02838 (  180)
  hydrogen bonds       : angle       4.52973 (  576)
  SS BOND              : bond        0.00295 (    7)
  SS BOND              : angle       0.67686 (   14)
  covalent geometry    : bond        0.00258 ( 4434)
  covalent geometry    : angle       0.59115 ( 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
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  112 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7941 (mm)
REVERT: A   26 ASN cc_start: 0.8437 (t0) cc_final: 0.8027 (t0)
REVERT: B   59 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6295 (pt0)
REVERT: B   68 LYS cc_start: 0.8298 (tppt) cc_final: 0.7953 (tppp)
  outliers start: 20
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1559
  time to fit residues: 17.4555
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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 C residue  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 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  113 THR
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:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   overall best weight:    0.7978

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.173242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.149801 restraints weight = 5389.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.04
r_work: 0.3644 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1909

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= 0.137
  Angle     :  0.603   8.052   6061  Z= 0.288
  Chirality :  0.042   0.320    669
  Planarity :  0.004   0.031    773
  Dihedral  :  6.854  55.146    690
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.58 %
    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:  0.22 (0.38), residues: 521
  helix:  2.31 (0.47), residues: 116
  sheet: -0.47 (0.37), residues: 200
  loop : -0.34 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 152 
 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   0.002   0.000   ARG A 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00325 (    2)
  link_NAG-ASN         : angle       0.82275 (    6)
  link_BETA1-4         : bond        0.00345 (    3)
  link_BETA1-4         : angle       1.52959 (    9)
  hydrogen bonds       : bond        0.02973 (  180)
  hydrogen bonds       : angle       4.52960 (  576)
  SS BOND              : bond        0.00274 (    7)
  SS BOND              : angle       0.66662 (   14)
  covalent geometry    : bond        0.00325 ( 4434)
  covalent geometry    : angle       0.60012 ( 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
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  112 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8068 (mm)
REVERT: A   26 ASN cc_start: 0.8378 (t0) cc_final: 0.8047 (t0)
REVERT: B   59 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6299 (pt0)
REVERT: B   68 LYS cc_start: 0.8228 (tppt) cc_final: 0.7938 (tppp)
  outliers start: 17
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1814
  time to fit residues: 20.5045
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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 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   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  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  199 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:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0040
   chunk 15 optimal weight:    0.0060
   chunk 30 optimal weight:    0.0370
   overall best weight:    0.3286

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.175926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149418 restraints weight = 5413.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.21
r_work: 0.3674 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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   0.029   4446  Z= 0.102
  Angle     :  0.583   8.339   6061  Z= 0.282
  Chirality :  0.041   0.291    669
  Planarity :  0.004   0.032    773
  Dihedral  :  6.635  54.243    690
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.86 %
    Favored  : 74.36 %
  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:  0.40 (0.38), residues: 521
  helix:  2.61 (0.47), residues: 116
  sheet: -0.41 (0.38), residues: 194
  loop : -0.28 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 100 
 HIS   0.004   0.001   HIS C  31 
 PHE   0.007   0.001   PHE B 101 
 TYR   0.011   0.001   TYR B 138 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    2)
  link_NAG-ASN         : angle       0.62784 (    6)
  link_BETA1-4         : bond        0.00351 (    3)
  link_BETA1-4         : angle       1.37600 (    9)
  hydrogen bonds       : bond        0.02583 (  180)
  hydrogen bonds       : angle       4.27453 (  576)
  SS BOND              : bond        0.00195 (    7)
  SS BOND              : angle       0.59896 (   14)
  covalent geometry    : bond        0.00237 ( 4434)
  covalent geometry    : angle       0.58128 ( 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
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  112 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7898 (mm)
REVERT: A   26 ASN cc_start: 0.8352 (t0) cc_final: 0.7952 (t0)
REVERT: A   88 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.7805 (ttp-170)
REVERT: B   59 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6229 (pt0)
REVERT: B   68 LYS cc_start: 0.8259 (tppt) cc_final: 0.7936 (tppp)
  outliers start: 13
  outliers final: 11
  residues processed: 85
  average time/residue: 0.1700
  time to fit residues: 18.2489
Evaluate side-chains
  85 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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 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   14 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  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:    6.9990
   chunk 42 optimal weight:    0.0570
   chunk 11 optimal weight:    0.2980
   chunk 3 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.175197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148686 restraints weight = 5301.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.18
r_work: 0.3659 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3503 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4446  Z= 0.117
  Angle     :  0.587   8.350   6061  Z= 0.283
  Chirality :  0.041   0.285    669
  Planarity :  0.004   0.031    773
  Dihedral  :  6.642  54.726    690
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.14
  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:  0.43 (0.38), residues: 521
  helix:  2.56 (0.47), residues: 116
  sheet: -0.37 (0.38), residues: 194
  loop : -0.24 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 100 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.006   0.001   PHE B 101 
 TYR   0.010   0.001   TYR B 138 
 ARG   0.002   0.000   ARG A  90 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00232 (    2)
  link_NAG-ASN         : angle       0.74803 (    6)
  link_BETA1-4         : bond        0.00353 (    3)
  link_BETA1-4         : angle       1.42423 (    9)
  hydrogen bonds       : bond        0.02680 (  180)
  hydrogen bonds       : angle       4.27442 (  576)
  SS BOND              : bond        0.00232 (    7)
  SS BOND              : angle       0.57680 (   14)
  covalent geometry    : bond        0.00274 ( 4434)
  covalent geometry    : angle       0.58516 ( 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
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASN cc_start: 0.8371 (t0) cc_final: 0.7978 (t0)
REVERT: B   59 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6262 (pt0)
REVERT: B   68 LYS cc_start: 0.8235 (tppt) cc_final: 0.7939 (tppp)
  outliers start: 14
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1662
  time to fit residues: 18.3070
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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  149 SER
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain B residue   14 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  134 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0970
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.175081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151261 restraints weight = 5371.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.05
r_work: 0.3672 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4446  Z= 0.129
  Angle     :  0.603   8.327   6061  Z= 0.292
  Chirality :  0.042   0.286    669
  Planarity :  0.004   0.031    773
  Dihedral  :  6.668  54.800    690
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.08 %
    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:  0.37 (0.38), residues: 521
  helix:  2.48 (0.47), residues: 116
  sheet: -0.38 (0.38), residues: 194
  loop : -0.29 (0.44), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 152 
 HIS   0.003   0.001   HIS C  31 
 PHE   0.007   0.001   PHE B 153 
 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        0.00238 (    2)
  link_NAG-ASN         : angle       0.74799 (    6)
  link_BETA1-4         : bond        0.00338 (    3)
  link_BETA1-4         : angle       1.41543 (    9)
  hydrogen bonds       : bond        0.02757 (  180)
  hydrogen bonds       : angle       4.31133 (  576)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       0.57098 (   14)
  covalent geometry    : bond        0.00304 ( 4434)
  covalent geometry    : angle       0.60048 ( 6032)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2794.34 seconds
wall clock time: 48 minutes 53.72 seconds (2933.72 seconds total)