Starting phenix.real_space_refine
on Tue Mar  3 13:52:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n62_24192/03_2026/7n62_24192_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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      17      5.16       5
     C    3569      2.51       5
     N     933      2.21       5
     O    1094      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5613
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2235
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 14, 'TRANS': 262}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1689
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1619
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.44, per 1000 atoms: 0.26
  Number of scatterers: 5613
  At special positions: 0
  Unit cell: (64.35, 95.7, 122.925, 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      17     16.00
     O    1094      8.00
     N     933      7.00
     C    3569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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
    NAG-ASN
      " NAG A1301 " - " ASN A  17 "
      " NAG A1302 " - " ASN A  61 "
      " NAG A1303 " - " ASN A 122 "
      " NAG A1304 " - " ASN A 165 "
      " NAG A1305 " - " ASN A 234 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 360.7 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 16 sheets defined
      5.3% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.558A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 195 through 199
    Processing helix  chain 'L' and resid 29 through 32
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.775A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 182 through 188
      removed outlier: 4.097A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28
      removed outlier: 3.628A  pdb=" N   LYS A 195 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.649A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 5.651A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145
      removed outlier: 4.062A  pdb=" N   TYR A 144 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET A 153 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.865A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 132 through 133
      removed outlier: 4.376A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL H 192 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.530A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.631A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.731A  pdb=" N   LYS L 145 " --> pdb=" O   THR L 197 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   CYS L 194 " --> pdb=" O   LYS L 207 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.52 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: 1779
        1.34 -     1.46: 1526
        1.46 -     1.59: 2431
        1.59 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" N   GLU H   6 "
       pdb=" CA  GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.33e+00
  bond pdb=" N   ASP A 253 "
       pdb=" CA  ASP A 253 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.50e-02 4.44e+03 5.06e+00
  bond pdb=" C   ALA H  92 "
       pdb=" N   VAL H  93 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.24e-02 6.50e+03 2.83e+00
  bond pdb=" CB  PRO H 159 "
       pdb=" CG  PRO H 159 "
    ideal  model  delta    sigma   weight residual
    1.506  1.567 -0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CB  TRP H  36 "
       pdb=" CG  TRP H  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.455  0.043 3.10e-02 1.04e+03 1.97e+00
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 7408
        1.64 -     3.28: 354
        3.28 -     4.92: 51
        4.92 -     6.56: 14
        6.56 -     8.20: 5
  Bond angle restraints: 7832
  Sorted by residual:
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     120.60  113.12    7.48 2.20e+00 2.07e-01 1.16e+01
  angle pdb=" N   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" C   TYR A 144 "
      ideal   model   delta    sigma   weight residual
     108.46  113.39   -4.93 1.51e+00 4.39e-01 1.07e+01
  angle pdb=" CA  PRO H 159 "
        pdb=" N   PRO H 159 "
        pdb=" CD  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     111.50  107.46    4.04 1.40e+00 5.10e-01 8.34e+00
  angle pdb=" CA  GLU A  96 "
        pdb=" CB  GLU A  96 "
        pdb=" CG  GLU A  96 "
      ideal   model   delta    sigma   weight residual
     114.10  119.83   -5.73 2.00e+00 2.50e-01 8.21e+00
  angle pdb=" C   GLU H 158 "
        pdb=" N   PRO H 159 "
        pdb=" CA  PRO H 159 "
      ideal   model   delta    sigma   weight residual
     127.00  133.63   -6.63 2.40e+00 1.74e-01 7.62e+00
  ... (remaining 7827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3112
       17.83 -    35.66: 280
       35.66 -    53.49: 54
       53.49 -    71.32: 8
       71.32 -    89.14: 4
  Dihedral angle restraints: 3458
    sinusoidal: 1396
      harmonic: 2062
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.85   56.15     1      1.00e+01 1.00e-02 4.25e+01
  dihedral pdb=" CA  THR A  19 "
           pdb=" C   THR A  19 "
           pdb=" N   THR A  20 "
           pdb=" CA  THR A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.77   27.23     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  PRO A  82 "
           pdb=" C   PRO A  82 "
           pdb=" N   VAL A  83 "
           pdb=" CA  VAL A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.13   25.87     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 3455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 839
       0.106 -    0.213: 32
       0.213 -    0.319: 2
       0.319 -    0.425: 1
       0.425 -    0.532: 1
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" C1  NAG A1304 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1304 "
            pdb=" O5  NAG A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CB  ILE A 210 "
            pdb=" CA  ILE A 210 "
            pdb=" CG1 ILE A 210 "
            pdb=" CG2 ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  ILE L  76 "
            pdb=" CA  ILE L  76 "
            pdb=" CG1 ILE L  76 "
            pdb=" CG2 ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 872 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L 119 "   -0.061 5.00e-02 4.00e+02   9.15e-02 1.34e+01
        pdb=" N   PRO L 120 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO L 120 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO L 120 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "   -0.057 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO H 159 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H 135 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO H 136 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO H 136 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 136 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 764
        2.74 -     3.28: 6066
        3.28 -     3.82: 9555
        3.82 -     4.36: 11231
        4.36 -     4.90: 18714
  Nonbonded interactions: 46330
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 156 "
            pdb=" OH  TYR A 160 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLN L 166 "
            pdb=" OG  SER L 171 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH2 ARG A 158 "
            pdb=" OD1 ASP H 101 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   GLN A  14 "
            pdb=" NH1 ARG A 158 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   TYR L 186 "
            pdb=" OH  TYR L 192 "
     model   vdw
     2.229 3.040
  ... (remaining 46325 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.060
  Find NCS groups from input model:        0.030
  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:           0.010
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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   0.061   5769  Z= 0.297
  Angle     :  0.855  14.301   7859  Z= 0.450
  Chirality :  0.053   0.532    875
  Planarity :  0.006   0.092   1000
  Dihedral  : 13.902  89.144   2126
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 21.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.31), residues: 706
  helix: -2.65 (1.15), residues: 14
  sheet: -1.13 (0.31), residues: 269
  loop : -2.35 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  72 
 TYR   0.035   0.002   TYR A 144 
 PHE   0.020   0.002   PHE L  72 
 TRP   0.025   0.003   TRP A 258 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 5758)
  covalent geometry    : angle       0.82457 ( 7832)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       1.43064 (   12)
  hydrogen bonds       : bond        0.28264 (  169)
  hydrogen bonds       : angle      11.20079 (  429)
  link_NAG-ASN         : bond        0.00803 (    5)
  link_NAG-ASN         : angle       5.12659 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 THR cc_start: 0.6470 (t) cc_final: 0.6260 (t)
REVERT: A   56 LEU cc_start: 0.9064 (tp) cc_final: 0.8690 (tp)
REVERT: A  100 ILE cc_start: 0.9421 (tt) cc_final: 0.9203 (tt)
REVERT: H   90 ASP cc_start: 0.9094 (m-30) cc_final: 0.8846 (m-30)
REVERT: H   99 ASP cc_start: 0.9255 (t0) cc_final: 0.8997 (t0)
REVERT: H  104 TYR cc_start: 0.8107 (t80) cc_final: 0.7561 (t80)
REVERT: L   88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9139 (m-80)
REVERT: L  139 PHE cc_start: 0.8581 (p90) cc_final: 0.8362 (p90)
REVERT: L  142 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8165 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0723
  time to fit residues: 12.2340
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 ASN
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.073649 restraints weight = 14095.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.076559 restraints weight = 7210.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.078509 restraints weight = 4771.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.079661 restraints weight = 3653.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.080530 restraints weight = 3094.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   5769  Z= 0.205
  Angle     :  0.801  12.513   7859  Z= 0.411
  Chirality :  0.051   0.463    875
  Planarity :  0.006   0.072   1000
  Dihedral  :  6.972  56.953    880
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.16 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.30), residues: 706
  helix: -1.72 (1.21), residues: 14
  sheet: -1.04 (0.29), residues: 273
  loop : -2.30 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 108 
 TYR   0.024   0.002   TYR A 144 
 PHE   0.016   0.002   PHE L  72 
 TRP   0.018   0.002   TRP A 258 
 HIS   0.008   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 5758)
  covalent geometry    : angle       0.77846 ( 7832)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       1.19155 (   12)
  hydrogen bonds       : bond        0.04865 (  169)
  hydrogen bonds       : angle       8.05360 (  429)
  link_NAG-ASN         : bond        0.00765 (    5)
  link_NAG-ASN         : angle       4.31300 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9021 (tp) cc_final: 0.8635 (tp)
REVERT: A   91 TYR cc_start: 0.9273 (t80) cc_final: 0.8878 (t80)
REVERT: A  156 GLU cc_start: 0.8573 (pt0) cc_final: 0.8182 (pt0)
REVERT: H   90 ASP cc_start: 0.8982 (m-30) cc_final: 0.8690 (m-30)
REVERT: L   88 TYR cc_start: 0.9402 (m-80) cc_final: 0.9156 (m-80)
REVERT: L   90 GLN cc_start: 0.8577 (tt0) cc_final: 0.8256 (tt0)
REVERT: L  139 PHE cc_start: 0.8656 (p90) cc_final: 0.8328 (p90)
REVERT: L  142 ARG cc_start: 0.8475 (tpt90) cc_final: 0.8131 (tpt90)
  outliers start: 5
  outliers final: 3
  residues processed: 117
  average time/residue: 0.0667
  time to fit residues: 10.3640
Evaluate side-chains
  100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.104807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.075456 restraints weight = 13944.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.078402 restraints weight = 7100.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.080378 restraints weight = 4664.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.081654 restraints weight = 3545.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082371 restraints weight = 2978.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5769  Z= 0.155
  Angle     :  0.747  11.437   7859  Z= 0.379
  Chirality :  0.050   0.434    875
  Planarity :  0.006   0.065   1000
  Dihedral  :  6.455  52.453    880
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.91 %
    Favored  : 89.09 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.53 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.30), residues: 706
  helix: -1.39 (1.25), residues: 14
  sheet: -0.90 (0.29), residues: 278
  loop : -2.15 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 214 
 TYR   0.017   0.001   TYR A 144 
 PHE   0.024   0.002   PHE L 209 
 TRP   0.017   0.002   TRP A 258 
 HIS   0.003   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5758)
  covalent geometry    : angle       0.72604 ( 7832)
  SS BOND              : bond        0.00399 (    6)
  SS BOND              : angle       1.57309 (   12)
  hydrogen bonds       : bond        0.03745 (  169)
  hydrogen bonds       : angle       7.43740 (  429)
  link_NAG-ASN         : bond        0.00703 (    5)
  link_NAG-ASN         : angle       3.89450 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9059 (p)
REVERT: A   56 LEU cc_start: 0.8948 (tp) cc_final: 0.8551 (tp)
REVERT: A  154 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: A  156 GLU cc_start: 0.8462 (pt0) cc_final: 0.8133 (pt0)
REVERT: A  157 PHE cc_start: 0.8712 (m-80) cc_final: 0.8463 (m-10)
REVERT: A  194 PHE cc_start: 0.8905 (m-80) cc_final: 0.8698 (m-10)
REVERT: H   90 ASP cc_start: 0.8988 (m-30) cc_final: 0.8665 (m-30)
REVERT: L   88 TYR cc_start: 0.9392 (m-80) cc_final: 0.9109 (m-80)
REVERT: L   90 GLN cc_start: 0.8602 (tt0) cc_final: 0.8319 (tt0)
REVERT: L  139 PHE cc_start: 0.8628 (p90) cc_final: 0.8359 (p90)
REVERT: L  140 TYR cc_start: 0.7835 (t80) cc_final: 0.7634 (t80)
REVERT: L  142 ARG cc_start: 0.8452 (tpt90) cc_final: 0.8005 (tpt90)
  outliers start: 10
  outliers final: 7
  residues processed: 119
  average time/residue: 0.0768
  time to fit residues: 11.9548
Evaluate side-chains
  101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain L residue  117 ILE
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 50 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
A  52 GLN
A 115 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.073877 restraints weight = 14002.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.076954 restraints weight = 7020.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.078918 restraints weight = 4578.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.080254 restraints weight = 3482.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.080724 restraints weight = 2920.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5769  Z= 0.214
  Angle     :  0.756  10.772   7859  Z= 0.382
  Chirality :  0.049   0.429    875
  Planarity :  0.005   0.065   1000
  Dihedral  :  6.234  40.919    880
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.31 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.30), residues: 706
  helix: -1.14 (1.30), residues: 14
  sheet: -1.03 (0.28), residues: 302
  loop : -2.15 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 214 
 TYR   0.029   0.002   TYR A 144 
 PHE   0.017   0.002   PHE L  72 
 TRP   0.020   0.002   TRP A 258 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 5758)
  covalent geometry    : angle       0.73624 ( 7832)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.53797 (   12)
  hydrogen bonds       : bond        0.03568 (  169)
  hydrogen bonds       : angle       7.21448 (  429)
  link_NAG-ASN         : bond        0.00588 (    5)
  link_NAG-ASN         : angle       3.76009 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9042 (p)
REVERT: A   56 LEU cc_start: 0.9030 (tp) cc_final: 0.8642 (tp)
REVERT: A  154 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: A  156 GLU cc_start: 0.8583 (pt0) cc_final: 0.8189 (pt0)
REVERT: A  157 PHE cc_start: 0.8788 (m-80) cc_final: 0.8582 (m-10)
REVERT: A  191 GLU cc_start: 0.8641 (tt0) cc_final: 0.8381 (mt-10)
REVERT: H   90 ASP cc_start: 0.8998 (m-30) cc_final: 0.8657 (m-30)
REVERT: H  101 ASP cc_start: 0.8708 (t0) cc_final: 0.8430 (t0)
REVERT: L   88 TYR cc_start: 0.9464 (m-80) cc_final: 0.9224 (m-80)
REVERT: L   90 GLN cc_start: 0.8806 (tt0) cc_final: 0.8514 (tt0)
REVERT: L  139 PHE cc_start: 0.8621 (p90) cc_final: 0.8357 (p90)
REVERT: L  142 ARG cc_start: 0.8466 (tpt90) cc_final: 0.7978 (tpt90)
  outliers start: 17
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0748
  time to fit residues: 11.4914
Evaluate side-chains
  117 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue  117 ILE
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 47 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.102034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.071866 restraints weight = 14518.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.074938 restraints weight = 7218.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.076934 restraints weight = 4665.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.078235 restraints weight = 3525.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.079059 restraints weight = 2946.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   5769  Z= 0.287
  Angle     :  0.780  10.398   7859  Z= 0.400
  Chirality :  0.051   0.435    875
  Planarity :  0.006   0.067   1000
  Dihedral  :  6.384  34.606    880
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.96 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.30), residues: 706
  helix: -1.40 (1.33), residues: 14
  sheet: -1.09 (0.29), residues: 280
  loop : -2.14 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 158 
 TYR   0.038   0.002   TYR A 144 
 PHE   0.023   0.002   PHE L  72 
 TRP   0.022   0.002   TRP A 258 
 HIS   0.004   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 5758)
  covalent geometry    : angle       0.76177 ( 7832)
  SS BOND              : bond        0.00491 (    6)
  SS BOND              : angle       1.56658 (   12)
  hydrogen bonds       : bond        0.03555 (  169)
  hydrogen bonds       : angle       7.20246 (  429)
  link_NAG-ASN         : bond        0.00532 (    5)
  link_NAG-ASN         : angle       3.69292 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   36 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9051 (p)
REVERT: A   56 LEU cc_start: 0.9034 (tp) cc_final: 0.8679 (tp)
REVERT: A  154 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: A  156 GLU cc_start: 0.8609 (pt0) cc_final: 0.8163 (pt0)
REVERT: H   90 ASP cc_start: 0.9052 (m-30) cc_final: 0.8733 (m-30)
REVERT: H  101 ASP cc_start: 0.8705 (t0) cc_final: 0.8363 (t0)
REVERT: L   88 TYR cc_start: 0.9479 (m-80) cc_final: 0.9278 (m-80)
REVERT: L  139 PHE cc_start: 0.8565 (p90) cc_final: 0.8333 (p90)
REVERT: L  142 ARG cc_start: 0.8463 (tpt90) cc_final: 0.7988 (tpt90)
REVERT: L  192 TYR cc_start: 0.8502 (m-10) cc_final: 0.8220 (m-10)
  outliers start: 23
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0704
  time to fit residues: 11.1584
Evaluate side-chains
  118 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 TYR
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue  117 ILE
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0870
   chunk 20 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.106597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.076766 restraints weight = 14058.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.079903 restraints weight = 6929.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.081899 restraints weight = 4444.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.082981 restraints weight = 3349.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.083993 restraints weight = 2843.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5769  Z= 0.132
  Angle     :  0.750   9.977   7859  Z= 0.376
  Chirality :  0.049   0.390    875
  Planarity :  0.005   0.064   1000
  Dihedral  :  5.808  32.276    880
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.91 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.30), residues: 706
  helix: -1.12 (1.37), residues: 14
  sheet: -0.98 (0.28), residues: 306
  loop : -2.00 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 214 
 TYR   0.025   0.001   TYR L 140 
 PHE   0.015   0.002   PHE H 176 
 TRP   0.019   0.002   TRP A 258 
 HIS   0.002   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5758)
  covalent geometry    : angle       0.72943 ( 7832)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       2.59811 (   12)
  hydrogen bonds       : bond        0.03098 (  169)
  hydrogen bonds       : angle       6.85373 (  429)
  link_NAG-ASN         : bond        0.00689 (    5)
  link_NAG-ASN         : angle       3.37641 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 ASN cc_start: 0.8926 (t0) cc_final: 0.8676 (t0)
REVERT: A   56 LEU cc_start: 0.8971 (tp) cc_final: 0.8638 (tp)
REVERT: A   91 TYR cc_start: 0.9240 (t80) cc_final: 0.8920 (t80)
REVERT: A  140 PHE cc_start: 0.9627 (p90) cc_final: 0.8968 (p90)
REVERT: A  144 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7234 (p90)
REVERT: A  154 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: A  157 PHE cc_start: 0.8726 (m-80) cc_final: 0.8518 (m-10)
REVERT: A  191 GLU cc_start: 0.8529 (tt0) cc_final: 0.8058 (mm-30)
REVERT: A  202 LYS cc_start: 0.8610 (mttp) cc_final: 0.8339 (mttp)
REVERT: H   90 ASP cc_start: 0.8955 (m-30) cc_final: 0.8596 (m-30)
REVERT: H  101 ASP cc_start: 0.8404 (t0) cc_final: 0.8188 (t0)
REVERT: H  204 TYR cc_start: 0.6334 (m-80) cc_final: 0.5962 (m-10)
REVERT: L   88 TYR cc_start: 0.9389 (m-80) cc_final: 0.9096 (m-80)
REVERT: L   90 GLN cc_start: 0.8701 (tt0) cc_final: 0.8429 (tt0)
REVERT: L  139 PHE cc_start: 0.8566 (p90) cc_final: 0.8297 (p90)
REVERT: L  142 ARG cc_start: 0.8385 (tpt90) cc_final: 0.7912 (tpt90)
REVERT: L  192 TYR cc_start: 0.8625 (m-10) cc_final: 0.8369 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 142
  average time/residue: 0.0766
  time to fit residues: 14.1493
Evaluate side-chains
  123 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 TYR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.104599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.074992 restraints weight = 14424.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.078018 restraints weight = 7219.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.080008 restraints weight = 4706.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.081156 restraints weight = 3571.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082029 restraints weight = 3013.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5769  Z= 0.198
  Angle     :  0.740   9.641   7859  Z= 0.376
  Chirality :  0.049   0.400    875
  Planarity :  0.005   0.063   1000
  Dihedral  :  5.852  32.032    880
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.39 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.30), residues: 706
  helix: -0.88 (1.46), residues: 14
  sheet: -1.01 (0.28), residues: 302
  loop : -2.07 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 214 
 TYR   0.025   0.002   TYR A 144 
 PHE   0.020   0.002   PHE L  72 
 TRP   0.019   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 5758)
  covalent geometry    : angle       0.72206 ( 7832)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       2.04499 (   12)
  hydrogen bonds       : bond        0.03154 (  169)
  hydrogen bonds       : angle       6.82753 (  429)
  link_NAG-ASN         : bond        0.00561 (    5)
  link_NAG-ASN         : angle       3.31161 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8953 (tp) cc_final: 0.8605 (tp)
REVERT: A  144 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (p90)
REVERT: A  154 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7838 (mt-10)
REVERT: A  157 PHE cc_start: 0.8738 (m-80) cc_final: 0.8490 (m-10)
REVERT: A  202 LYS cc_start: 0.8689 (mttp) cc_final: 0.8348 (mttp)
REVERT: H   90 ASP cc_start: 0.8969 (m-30) cc_final: 0.8659 (m-30)
REVERT: H  101 ASP cc_start: 0.8464 (t0) cc_final: 0.8250 (t0)
REVERT: L   88 TYR cc_start: 0.9414 (m-80) cc_final: 0.9166 (m-80)
REVERT: L   90 GLN cc_start: 0.8647 (tt0) cc_final: 0.8373 (tt0)
REVERT: L  139 PHE cc_start: 0.8581 (p90) cc_final: 0.8296 (p90)
REVERT: L  142 ARG cc_start: 0.8397 (tpt90) cc_final: 0.7919 (tpt90)
  outliers start: 20
  outliers final: 13
  residues processed: 133
  average time/residue: 0.0790
  time to fit residues: 13.6822
Evaluate side-chains
  120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0270
   chunk 20 optimal weight:    0.0040
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.2056

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 174 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.107843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.078178 restraints weight = 14051.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.081402 restraints weight = 6854.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.083450 restraints weight = 4386.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.084697 restraints weight = 3309.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.085634 restraints weight = 2771.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   5769  Z= 0.147
  Angle     :  0.748   9.561   7859  Z= 0.378
  Chirality :  0.049   0.385    875
  Planarity :  0.005   0.062   1000
  Dihedral  :  5.633  30.432    880
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.18 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.31), residues: 706
  helix: -1.14 (1.38), residues: 14
  sheet: -0.90 (0.29), residues: 302
  loop : -2.01 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 246 
 TYR   0.033   0.002   TYR L 140 
 PHE   0.018   0.002   PHE L  84 
 TRP   0.023   0.002   TRP A 258 
 HIS   0.002   0.001   HIS H 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 5758)
  covalent geometry    : angle       0.73280 ( 7832)
  SS BOND              : bond        0.00305 (    6)
  SS BOND              : angle       1.69122 (   12)
  hydrogen bonds       : bond        0.03081 (  169)
  hydrogen bonds       : angle       6.77196 (  429)
  link_NAG-ASN         : bond        0.00601 (    5)
  link_NAG-ASN         : angle       3.25300 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8984 (tp) cc_final: 0.8649 (tp)
REVERT: A  140 PHE cc_start: 0.9613 (p90) cc_final: 0.8958 (p90)
REVERT: A  144 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7107 (p90)
REVERT: A  154 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: A  157 PHE cc_start: 0.8637 (m-80) cc_final: 0.8424 (m-10)
REVERT: H   90 ASP cc_start: 0.8950 (m-30) cc_final: 0.8655 (m-30)
REVERT: H  101 ASP cc_start: 0.8399 (t0) cc_final: 0.8165 (t0)
REVERT: H  104 TYR cc_start: 0.8001 (t80) cc_final: 0.7784 (t80)
REVERT: H  204 TYR cc_start: 0.6252 (m-80) cc_final: 0.5949 (m-10)
REVERT: L   88 TYR cc_start: 0.9392 (m-80) cc_final: 0.9096 (m-80)
REVERT: L   90 GLN cc_start: 0.8743 (tt0) cc_final: 0.8448 (tt0)
REVERT: L  139 PHE cc_start: 0.8453 (p90) cc_final: 0.8128 (p90)
REVERT: L  142 ARG cc_start: 0.8353 (tpt90) cc_final: 0.7889 (tpt90)
  outliers start: 17
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0731
  time to fit residues: 12.8626
Evaluate side-chains
  125 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 TYR
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  196 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0170
   chunk 67 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0030
   chunk 42 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 64 optimal weight:    8.9990
   overall best weight:    0.4030

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.080794 restraints weight = 13971.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.084116 restraints weight = 6876.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.086251 restraints weight = 4398.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.087635 restraints weight = 3307.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.088433 restraints weight = 2751.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5769  Z= 0.130
  Angle     :  0.758   9.663   7859  Z= 0.378
  Chirality :  0.049   0.373    875
  Planarity :  0.005   0.047   1000
  Dihedral  :  5.364  24.795    880
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 24.47 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.31), residues: 706
  helix: -1.06 (1.37), residues: 14
  sheet: -0.70 (0.30), residues: 285
  loop : -1.93 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 246 
 TYR   0.036   0.001   TYR L 140 
 PHE   0.017   0.002   PHE H 176 
 TRP   0.022   0.002   TRP A 258 
 HIS   0.002   0.001   HIS H 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5758)
  covalent geometry    : angle       0.74363 ( 7832)
  SS BOND              : bond        0.00507 (    6)
  SS BOND              : angle       1.56962 (   12)
  hydrogen bonds       : bond        0.03151 (  169)
  hydrogen bonds       : angle       6.55987 (  429)
  link_NAG-ASN         : bond        0.00658 (    5)
  link_NAG-ASN         : angle       3.22913 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8934 (tp) cc_final: 0.8580 (tp)
REVERT: A  140 PHE cc_start: 0.9575 (p90) cc_final: 0.8914 (p90)
REVERT: A  154 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7764 (mt-10)
REVERT: H   36 TRP cc_start: 0.8517 (m100) cc_final: 0.8257 (m100)
REVERT: H   90 ASP cc_start: 0.8872 (m-30) cc_final: 0.8625 (m-30)
REVERT: H  155 TYR cc_start: 0.8345 (p90) cc_final: 0.8063 (p90)
REVERT: H  161 THR cc_start: 0.8920 (m) cc_final: 0.8615 (p)
REVERT: L   31 SER cc_start: 0.9201 (t) cc_final: 0.8965 (t)
REVERT: L   33 TYR cc_start: 0.7679 (m-10) cc_final: 0.7463 (m-10)
REVERT: L   88 TYR cc_start: 0.9347 (m-80) cc_final: 0.8983 (m-80)
REVERT: L   90 GLN cc_start: 0.8697 (tt0) cc_final: 0.8413 (tt0)
REVERT: L  103 LYS cc_start: 0.8437 (tttp) cc_final: 0.8117 (tppt)
REVERT: L  139 PHE cc_start: 0.8405 (p90) cc_final: 0.8139 (p90)
REVERT: L  142 ARG cc_start: 0.8360 (tpt90) cc_final: 0.7831 (tpt90)
REVERT: L  145 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8775 (mmmm)
  outliers start: 15
  outliers final: 12
  residues processed: 152
  average time/residue: 0.0762
  time to fit residues: 15.1471
Evaluate side-chains
  131 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  196 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 69 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** H 210 HIS ** 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 = 0.3600 r_free = 0.3600 target = 0.110702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.080938 restraints weight = 14396.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.084263 restraints weight = 6962.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.086402 restraints weight = 4472.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087775 restraints weight = 3369.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.088638 restraints weight = 2801.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   5769  Z= 0.149
  Angle     :  0.761   9.440   7859  Z= 0.387
  Chirality :  0.049   0.374    875
  Planarity :  0.005   0.049   1000
  Dihedral  :  5.268  24.138    880
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.26 %
    Favored  : 71.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.31), residues: 706
  helix: -0.92 (1.42), residues: 14
  sheet: -0.59 (0.30), residues: 289
  loop : -1.98 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  16 
 TYR   0.035   0.002   TYR L 140 
 PHE   0.025   0.002   PHE A  92 
 TRP   0.023   0.002   TRP A 258 
 HIS   0.002   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5758)
  covalent geometry    : angle       0.74568 ( 7832)
  SS BOND              : bond        0.00550 (    6)
  SS BOND              : angle       1.92088 (   12)
  hydrogen bonds       : bond        0.03133 (  169)
  hydrogen bonds       : angle       6.52846 (  429)
  link_NAG-ASN         : bond        0.00584 (    5)
  link_NAG-ASN         : angle       3.18362 (   15)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8948 (tp) cc_final: 0.8572 (tp)
REVERT: A  140 PHE cc_start: 0.9580 (p90) cc_final: 0.8863 (p90)
REVERT: A  154 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: H   90 ASP cc_start: 0.8887 (m-30) cc_final: 0.8643 (m-30)
REVERT: H  161 THR cc_start: 0.8943 (m) cc_final: 0.8611 (p)
REVERT: L   31 SER cc_start: 0.9197 (t) cc_final: 0.8989 (t)
REVERT: L   88 TYR cc_start: 0.9374 (m-80) cc_final: 0.8999 (m-80)
REVERT: L   90 GLN cc_start: 0.8681 (tt0) cc_final: 0.8370 (tt0)
REVERT: L  139 PHE cc_start: 0.8375 (p90) cc_final: 0.8126 (p90)
REVERT: L  142 ARG cc_start: 0.8273 (tpt90) cc_final: 0.7763 (tpt90)
REVERT: L  192 TYR cc_start: 0.8630 (m-10) cc_final: 0.8372 (m-10)
  outliers start: 12
  outliers final: 11
  residues processed: 135
  average time/residue: 0.0693
  time to fit residues: 12.5716
Evaluate side-chains
  128 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   62 ASP
Chi-restraints excluded: chain H residue  138 SER
Chi-restraints excluded: chain H residue  193 THR
Chi-restraints excluded: chain H residue  206 CYS
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue  196 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:   40.0000
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 68 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 21 optimal weight:    6.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
H 202 GLN
** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.108866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.079175 restraints weight = 13969.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.082399 restraints weight = 6906.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.084512 restraints weight = 4457.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.085830 restraints weight = 3359.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.086612 restraints weight = 2804.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   5769  Z= 0.181
  Angle     :  0.754   9.303   7859  Z= 0.384
  Chirality :  0.049   0.374    875
  Planarity :  0.005   0.051   1000
  Dihedral  :  5.383  24.786    880
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 25.93 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.31), residues: 706
  helix: -0.88 (1.44), residues: 14
  sheet: -0.67 (0.30), residues: 295
  loop : -1.97 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  16 
 TYR   0.028   0.002   TYR L 140 
 PHE   0.034   0.002   PHE A 133 
 TRP   0.016   0.002   TRP A 258 
 HIS   0.002   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 5758)
  covalent geometry    : angle       0.73868 ( 7832)
  SS BOND              : bond        0.00518 (    6)
  SS BOND              : angle       2.00971 (   12)
  hydrogen bonds       : bond        0.03234 (  169)
  hydrogen bonds       : angle       6.50117 (  429)
  link_NAG-ASN         : bond        0.00506 (    5)
  link_NAG-ASN         : angle       3.12018 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1120.02 seconds
wall clock time: 20 minutes 3.22 seconds (1203.22 seconds total)