Starting phenix.real_space_refine
on Fri Aug 22 17:59:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iow_35627/08_2025/8iow_35627.cif"
  }
  resolution = 3.2
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3017 atoms to isotropic.
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      18      5.16       5
     C    2628      2.51       5
     N     721      2.21       5
     O     811      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4178
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "I"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 863
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 6, 'TRANS': 97}
    Chain: "D2"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 107
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1619
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200}
    Chain: "H"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1561
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 11, 'TRANS': 195}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.96, per 1000 atoms: 0.23
  Number of scatterers: 4178
  At special positions: 0
  Unit cell: (58.22, 67.24, 104.96, 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      18     16.00
     O     811      8.00
     N     721      7.00
     C    2628      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYSD2 121 " - pdb=" SG  CYSD2 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " 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 I 401 " - " ASN I 221 "
      " NAG I 402 " - " ASN I 245 "
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 119.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  994

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 15 sheets defined
      6.7% alpha, 36.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'L' and resid 50 through 52
      No H-bonds generated for 'chain 'L' and resid 50 through 52'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.300A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
      removed outlier: 3.945A  pdb=" N   SER L 127 " --> pdb=" O   GLU L 123 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLY L 128 " --> pdb=" O   GLN L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 189
      removed outlier: 4.049A  pdb=" N   HIS L 189 " --> pdb=" O   ASP L 185 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.686A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 192
    Processing helix  chain 'H' and resid 205 through 207
      No H-bonds generated for 'chain 'H' and resid 205 through 207'
    Processing sheet with id=AA1, first strand: chain 'I' and resid 223 through 225
    Processing sheet with id=AA2, first strand: chain 'I' and resid 266 through 269
      removed outlier: 3.856A  pdb=" N   THR I 266 " --> pdb=" O   TYR I 257 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 289 through 290
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.959A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER L  65 " --> pdb=" O   THR L  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.423A  pdb=" N   VAL L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 46
    Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49
    Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.604A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 155
      removed outlier: 4.426A  pdb=" N   TRP L 148 " --> pdb=" O   GLN L 155 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS L 207 " --> pdb=" O   CYS L 194 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.720A  pdb=" N   MET H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   GLY H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY H  50 " --> pdb=" O   GLY H  59 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY H  59 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 73
    Processing sheet with id=AB4, first strand: chain 'H' and resid 123 through 127
      removed outlier: 5.034A  pdb=" N   ALA H 140 " --> pdb=" O   VAL H 187 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL H 187 " --> pdb=" O   ALA H 140 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   GLY H 142 " --> pdb=" O   VAL H 185 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   VAL H 185 " --> pdb=" O   GLY H 142 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU H 144 " --> pdb=" O   SER H 183 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   SER H 183 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   LYS H 146 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   LEU H 181 " --> pdb=" O   LYS H 146 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 123 through 127
      removed outlier: 5.034A  pdb=" N   ALA H 140 " --> pdb=" O   VAL H 187 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL H 187 " --> pdb=" O   ALA H 140 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   GLY H 142 " --> pdb=" O   VAL H 185 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   VAL H 185 " --> pdb=" O   GLY H 142 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU H 144 " --> pdb=" O   SER H 183 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   SER H 183 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   LYS H 146 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   LEU H 181 " --> pdb=" O   LYS H 146 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 157
      removed outlier: 3.547A  pdb=" N   THR H 154 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR H 197 " --> pdb=" O   VAL H 214 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS H 212 " --> pdb=" O   CYS H 199 " (cutoff:3.500A)

    126 hydrogen bonds defined for protein.
    300 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: 0.46

  Time building geometry restraints manager: 0.34 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: 1330
        1.34 -     1.46: 973
        1.46 -     1.58: 1954
        1.58 -     1.69: 1
        1.69 -     1.81: 24
  Bond restraints: 4282
  Sorted by residual:
  bond pdb=" C1  NAG I 402 "
       pdb=" O5  NAG I 402 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" CA  VAL I 227 "
       pdb=" CB  VAL I 227 "
    ideal  model  delta    sigma   weight residual
    1.530  1.555 -0.025 1.11e-02 8.12e+03 4.99e+00
  bond pdb=" CB  PRO I 308 "
       pdb=" CG  PRO I 308 "
    ideal  model  delta    sigma   weight residual
    1.492  1.588 -0.096 5.00e-02 4.00e+02 3.69e+00
  bond pdb=" C1  NAG I 401 "
       pdb=" O5  NAG I 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" SD  MET I 269 "
       pdb=" CE  MET I 269 "
    ideal  model  delta    sigma   weight residual
    1.791  1.750  0.041 2.50e-02 1.60e+03 2.64e+00
  ... (remaining 4277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 5557
        2.04 -     4.07: 208
        4.07 -     6.11: 33
        6.11 -     8.15: 17
        8.15 -    10.19: 3
  Bond angle restraints: 5818
  Sorted by residual:
  angle pdb=" CA  PRO I 308 "
        pdb=" N   PRO I 308 "
        pdb=" CD  PRO I 308 "
      ideal   model   delta    sigma   weight residual
     112.00  105.65    6.35 1.40e+00 5.10e-01 2.06e+01
  angle pdb=" N   ILE L  29 "
        pdb=" CA  ILE L  29 "
        pdb=" C   ILE L  29 "
      ideal   model   delta    sigma   weight residual
     112.96  109.10    3.86 1.00e+00 1.00e+00 1.49e+01
  angle pdb=" C   GLY L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  128.20   -6.66 1.91e+00 2.74e-01 1.22e+01
  angle pdb=" CG  ARG H  26 "
        pdb=" CD  ARG H  26 "
        pdb=" NE  ARG H  26 "
      ideal   model   delta    sigma   weight residual
     112.00  119.57   -7.57 2.20e+00 2.07e-01 1.18e+01
  angle pdb=" CA  TYR I 257 "
        pdb=" CB  TYR I 257 "
        pdb=" CG  TYR I 257 "
      ideal   model   delta    sigma   weight residual
     113.90  120.07   -6.17 1.80e+00 3.09e-01 1.17e+01
  ... (remaining 5813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 2253
       16.03 -    32.05: 238
       32.05 -    48.08: 59
       48.08 -    64.10: 16
       64.10 -    80.13: 5
  Dihedral angle restraints: 2571
    sinusoidal: 1027
      harmonic: 1544
  Sorted by residual:
  dihedral pdb=" CA  VAL H 114 "
           pdb=" C   VAL H 114 "
           pdb=" N   SER H 115 "
           pdb=" CA  SER H 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.97  -28.03     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -39.25  -46.75     1      1.00e+01 1.00e-02 3.02e+01
  dihedral pdb=" CB  CYSD2 121 "
           pdb=" SG  CYSD2 121 "
           pdb=" SG  CYSD2 132 "
           pdb=" CB  CYSD2 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.40   45.40     1      1.00e+01 1.00e-02 2.86e+01
  ... (remaining 2568 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 536
       0.075 -    0.151: 95
       0.151 -    0.226: 4
       0.226 -    0.301: 4
       0.301 -    0.376: 2
  Chirality restraints: 641
  Sorted by residual:
  chirality pdb=" C1  NAG I 402 "
            pdb=" ND2 ASN I 245 "
            pdb=" C2  NAG I 402 "
            pdb=" O5  NAG I 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CB  THR I 266 "
            pdb=" CA  THR I 266 "
            pdb=" OG1 THR I 266 "
            pdb=" CG2 THR I 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.19    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CB  ILE I 213 "
            pdb=" CA  ILE I 213 "
            pdb=" CG1 ILE I 213 "
            pdb=" CG2 ILE I 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 638 not shown)

  Planarity restraints: 747
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER I 307 "    0.090 5.00e-02 4.00e+02   1.32e-01 2.80e+01
        pdb=" N   PRO I 308 "   -0.229 5.00e-02 4.00e+02
        pdb=" CA  PRO I 308 "    0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO I 308 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  53 "   -0.034 2.00e-02 2.50e+03   2.88e-02 2.08e+01
        pdb=" CG  TRP H  53 "    0.074 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  53 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  53 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  53 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  53 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  53 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  53 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  53 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L  94 "   -0.048 5.00e-02 4.00e+02   7.31e-02 8.56e+00
        pdb=" N   PRO L  95 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 744 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1061
        2.80 -     3.32: 3522
        3.32 -     3.85: 7158
        3.85 -     4.37: 8163
        4.37 -     4.90: 14551
  Nonbonded interactions: 34455
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP L 170 "
            pdb=" OG1 THR L 172 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" NH1 ARG L  61 "
            pdb=" OD2 ASP L  82 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OD1 ASN H 202 "
            pdb=" NZ  LYS H 204 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   SERD2 128 "
            pdb=" OG  SERD2 128 "
     model   vdw
     2.335 3.040
  ... (remaining 34450 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.450
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
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      :  0.007   0.096   4289  Z= 0.281
  Angle     :  1.021  17.660   5834  Z= 0.538
  Chirality :  0.061   0.376    641
  Planarity :  0.009   0.132    745
  Dihedral  : 14.462  80.127   1562
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.22 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -2.31 (0.35), residues: 527
  helix: -2.63 (1.00), residues: 14
  sheet: -1.33 (0.34), residues: 218
  loop : -1.61 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG I 232 
 TYR   0.033   0.003   TYR L 173 
 PHE   0.036   0.004   PHE L  94 
 TRP   0.074   0.003   TRP H  53 
 HIS   0.005   0.001   HIS I 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 ( 4282)
  covalent geometry    : angle       0.98436 ( 5818)
  SS BOND              : bond        0.00421 (    5)
  SS BOND              : angle       1.31358 (   10)
  hydrogen bonds       : bond        0.27955 (  118)
  hydrogen bonds       : angle      12.12874 (  300)
  link_NAG-ASN         : bond        0.02258 (    2)
  link_NAG-ASN         : angle       8.37875 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.191 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1012
  time to fit residues: 8.9095
Evaluate side-chains
  65 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
I 242 HIS
L  90 GLN
** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 202 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.173331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146868 restraints weight = 4831.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.88
r_work: 0.3564 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4289  Z= 0.211
  Angle     :  0.713  11.569   5834  Z= 0.367
  Chirality :  0.048   0.295    641
  Planarity :  0.007   0.070    745
  Dihedral  :  6.951  48.051    617
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.11 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.82 (0.37), residues: 527
  helix: -2.02 (1.11), residues: 14
  sheet: -1.18 (0.35), residues: 215
  loop : -1.13 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I 258 
 TYR   0.014   0.002   TYR L 173 
 PHE   0.031   0.002   PHE H 149 
 TRP   0.013   0.001   TRP H  53 
 HIS   0.007   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 4282)
  covalent geometry    : angle       0.68873 ( 5818)
  SS BOND              : bond        0.00351 (    5)
  SS BOND              : angle       1.10252 (   10)
  hydrogen bonds       : bond        0.03907 (  118)
  hydrogen bonds       : angle       7.86097 (  300)
  link_NAG-ASN         : bond        0.01378 (    2)
  link_NAG-ASN         : angle       5.65412 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: L   79 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8055 (mm110)
REVERT: L  197 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8129 (p)
REVERT: L  208 SER cc_start: 0.8232 (m) cc_final: 0.7983 (p)
REVERT: H  180 SER cc_start: 0.8256 (t) cc_final: 0.7961 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1030
  time to fit residues: 10.3466
Evaluate side-chains
  79 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  237 THR
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain H residue   30 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
I 275 HIS
** L 189 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 = 0.3930 r_free = 0.3930 target = 0.168006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139370 restraints weight = 4729.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.09
r_work: 0.3437 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4289  Z= 0.189
  Angle     :  0.668  10.872   5834  Z= 0.341
  Chirality :  0.046   0.275    641
  Planarity :  0.006   0.067    745
  Dihedral  :  6.103  36.503    617
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.02 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.75 (0.36), residues: 527
  helix: -1.82 (1.09), residues: 14
  sheet: -1.08 (0.33), residues: 225
  loop : -1.11 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  26 
 TYR   0.014   0.002   TYR L 173 
 PHE   0.027   0.002   PHE H 149 
 TRP   0.007   0.001   TRP H 106 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 4282)
  covalent geometry    : angle       0.64588 ( 5818)
  SS BOND              : bond        0.00364 (    5)
  SS BOND              : angle       0.80600 (   10)
  hydrogen bonds       : bond        0.03245 (  118)
  hydrogen bonds       : angle       7.15826 (  300)
  link_NAG-ASN         : bond        0.01340 (    2)
  link_NAG-ASN         : angle       5.37258 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: I  276 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6865 (p90)
REVERT: L  182 SER cc_start: 0.8813 (t) cc_final: 0.8522 (p)
REVERT: L  190 LYS cc_start: 0.8306 (tmtt) cc_final: 0.8058 (tptp)
REVERT: L  197 THR cc_start: 0.8232 (m) cc_final: 0.7946 (p)
REVERT: L  208 SER cc_start: 0.8179 (m) cc_final: 0.7904 (p)
REVERT: H  180 SER cc_start: 0.8300 (t) cc_final: 0.8000 (p)
  outliers start: 10
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1007
  time to fit residues: 9.9865
Evaluate side-chains
  80 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain H residue   30 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
** H  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 200 ASN
H 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.133792 restraints weight = 4845.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.88
r_work: 0.3354 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.098   4289  Z= 0.354
  Angle     :  0.795   9.438   5834  Z= 0.408
  Chirality :  0.051   0.287    641
  Planarity :  0.006   0.070    745
  Dihedral  :  6.531  39.847    617
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.40 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -2.06 (0.36), residues: 527
  helix: -2.21 (1.00), residues: 14
  sheet: -1.29 (0.34), residues: 214
  loop : -1.33 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  26 
 TYR   0.016   0.002   TYR L 173 
 PHE   0.034   0.003   PHE H 149 
 TRP   0.011   0.002   TRP H 106 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00837 ( 4282)
  covalent geometry    : angle       0.77750 ( 5818)
  SS BOND              : bond        0.00661 (    5)
  SS BOND              : angle       1.24291 (   10)
  hydrogen bonds       : bond        0.03490 (  118)
  hydrogen bonds       : angle       7.42671 (  300)
  link_NAG-ASN         : bond        0.01146 (    2)
  link_NAG-ASN         : angle       5.01155 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7230 (mm)
REVERT: I  276 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7008 (p90)
REVERT: L  182 SER cc_start: 0.8814 (t) cc_final: 0.8512 (p)
REVERT: L  197 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8158 (p)
REVERT: L  208 SER cc_start: 0.8173 (m) cc_final: 0.7883 (p)
REVERT: H   53 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.8620 (p90)
REVERT: H  180 SER cc_start: 0.8315 (t) cc_final: 0.7888 (p)
REVERT: H  204 LYS cc_start: 0.8376 (tppt) cc_final: 0.8087 (mmtm)
  outliers start: 15
  outliers final: 8
  residues processed: 87
  average time/residue: 0.1016
  time to fit residues: 10.4033
Evaluate side-chains
  81 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  237 THR
Chi-restraints excluded: chain I residue  243 SER
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue  186 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 4 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.165096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.137205 restraints weight = 4802.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.03
r_work: 0.3481 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4289  Z= 0.145
  Angle     :  0.637   9.983   5834  Z= 0.324
  Chirality :  0.045   0.254    641
  Planarity :  0.005   0.061    745
  Dihedral  :  5.927  34.895    617
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.79 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.77 (0.36), residues: 527
  helix: -1.53 (1.15), residues: 14
  sheet: -1.10 (0.33), residues: 230
  loop : -1.13 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  26 
 TYR   0.013   0.001   TYR L  49 
 PHE   0.023   0.002   PHE H 149 
 TRP   0.011   0.001   TRP I 233 
 HIS   0.005   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4282)
  covalent geometry    : angle       0.61708 ( 5818)
  SS BOND              : bond        0.00322 (    5)
  SS BOND              : angle       0.68175 (   10)
  hydrogen bonds       : bond        0.02670 (  118)
  hydrogen bonds       : angle       6.58034 (  300)
  link_NAG-ASN         : bond        0.01328 (    2)
  link_NAG-ASN         : angle       4.98316 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7259 (mm)
REVERT: I  276 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6917 (p90)
REVERT: L  149 LYS cc_start: 0.8206 (mmtm) cc_final: 0.8001 (mmtm)
REVERT: L  182 SER cc_start: 0.8838 (t) cc_final: 0.8570 (p)
REVERT: L  197 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8007 (p)
  outliers start: 12
  outliers final: 6
  residues processed: 86
  average time/residue: 0.1074
  time to fit residues: 10.9490
Evaluate side-chains
  82 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  213 ILE
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   58 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
** H  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 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 = 0.3909 r_free = 0.3909 target = 0.166143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139263 restraints weight = 4884.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.91
r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4289  Z= 0.185
  Angle     :  0.659   9.638   5834  Z= 0.335
  Chirality :  0.046   0.255    641
  Planarity :  0.005   0.065    745
  Dihedral  :  5.886  35.743    617
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.22 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.71 (0.37), residues: 527
  helix: -1.36 (1.23), residues: 14
  sheet: -1.07 (0.33), residues: 230
  loop : -1.08 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  26 
 TYR   0.008   0.001   TYR L  49 
 PHE   0.026   0.002   PHE H 149 
 TRP   0.009   0.001   TRP I 233 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 4282)
  covalent geometry    : angle       0.63943 ( 5818)
  SS BOND              : bond        0.00359 (    5)
  SS BOND              : angle       0.93744 (   10)
  hydrogen bonds       : bond        0.02722 (  118)
  hydrogen bonds       : angle       6.54678 (  300)
  link_NAG-ASN         : bond        0.01202 (    2)
  link_NAG-ASN         : angle       4.88332 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7208 (mm)
REVERT: I  276 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6868 (p90)
REVERT: L  190 LYS cc_start: 0.8237 (tmtt) cc_final: 0.8036 (tptp)
REVERT: L  197 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8100 (p)
REVERT: H   53 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8494 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.1159
  time to fit residues: 11.4048
Evaluate side-chains
  84 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  213 ILE
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
** H  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 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 = 0.3888 r_free = 0.3888 target = 0.164330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137465 restraints weight = 4844.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.88
r_work: 0.3455 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4289  Z= 0.205
  Angle     :  0.669   9.455   5834  Z= 0.340
  Chirality :  0.046   0.252    641
  Planarity :  0.005   0.063    745
  Dihedral  :  5.936  36.906    617
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.17 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.72 (0.36), residues: 527
  helix: -1.55 (1.15), residues: 14
  sheet: -1.04 (0.33), residues: 233
  loop : -1.12 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  26 
 TYR   0.008   0.001   TYR L  86 
 PHE   0.027   0.002   PHE H 149 
 TRP   0.009   0.001   TRP I 233 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4282)
  covalent geometry    : angle       0.65002 ( 5818)
  SS BOND              : bond        0.00393 (    5)
  SS BOND              : angle       0.94772 (   10)
  hydrogen bonds       : bond        0.02767 (  118)
  hydrogen bonds       : angle       6.54012 (  300)
  link_NAG-ASN         : bond        0.01173 (    2)
  link_NAG-ASN         : angle       4.83438 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7212 (mm)
REVERT: I  276 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6842 (p90)
REVERT: L  190 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7990 (tptp)
REVERT: L  197 THR cc_start: 0.8373 (m) cc_final: 0.8111 (p)
REVERT: H   53 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.8512 (p90)
  outliers start: 12
  outliers final: 7
  residues processed: 84
  average time/residue: 0.1027
  time to fit residues: 10.3646
Evaluate side-chains
  82 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  213 ILE
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
** H  82 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 = 0.3876 r_free = 0.3876 target = 0.163077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.134554 restraints weight = 4809.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.06
r_work: 0.3447 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4289  Z= 0.188
  Angle     :  0.655   9.293   5834  Z= 0.333
  Chirality :  0.046   0.243    641
  Planarity :  0.005   0.064    745
  Dihedral  :  5.869  36.539    617
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.39 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.65 (0.37), residues: 527
  helix: -1.68 (1.11), residues: 14
  sheet: -1.01 (0.33), residues: 233
  loop : -1.04 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 232 
 TYR   0.009   0.001   TYR L  49 
 PHE   0.026   0.002   PHE H 149 
 TRP   0.011   0.001   TRP I 233 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 4282)
  covalent geometry    : angle       0.63713 ( 5818)
  SS BOND              : bond        0.00370 (    5)
  SS BOND              : angle       0.89161 (   10)
  hydrogen bonds       : bond        0.02660 (  118)
  hydrogen bonds       : angle       6.42609 (  300)
  link_NAG-ASN         : bond        0.01158 (    2)
  link_NAG-ASN         : angle       4.74055 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7272 (mm)
REVERT: I  276 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6929 (p90)
REVERT: L   79 GLN cc_start: 0.8400 (mm110) cc_final: 0.8061 (mm110)
REVERT: L  197 THR cc_start: 0.8366 (m) cc_final: 0.8049 (p)
REVERT: H   53 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.8496 (p90)
REVERT: H   83 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7121 (mtt)
  outliers start: 14
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1021
  time to fit residues: 10.4405
Evaluate side-chains
  86 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  213 ILE
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  255 LEU
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  180 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0470
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0770
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
** H  82 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 = 0.3938 r_free = 0.3938 target = 0.168935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142119 restraints weight = 4824.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.91
r_work: 0.3511 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4289  Z= 0.148
  Angle     :  0.627   9.245   5834  Z= 0.319
  Chirality :  0.045   0.229    641
  Planarity :  0.005   0.063    745
  Dihedral  :  5.677  34.105    617
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.48 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.51 (0.37), residues: 527
  helix: -1.65 (1.11), residues: 14
  sheet: -0.87 (0.33), residues: 232
  loop : -1.00 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  26 
 TYR   0.011   0.001   TYR L  49 
 PHE   0.023   0.002   PHE H 149 
 TRP   0.010   0.001   TRP I 233 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4282)
  covalent geometry    : angle       0.60900 ( 5818)
  SS BOND              : bond        0.00298 (    5)
  SS BOND              : angle       0.74755 (   10)
  hydrogen bonds       : bond        0.02521 (  118)
  hydrogen bonds       : angle       6.21221 (  300)
  link_NAG-ASN         : bond        0.01149 (    2)
  link_NAG-ASN         : angle       4.64550 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: I  276 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6905 (p90)
REVERT: L   79 GLN cc_start: 0.8380 (mm110) cc_final: 0.8107 (mm110)
REVERT: L  197 THR cc_start: 0.8344 (m) cc_final: 0.8088 (p)
REVERT: H   53 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.8386 (p90)
REVERT: H   83 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7063 (mtt)
  outliers start: 12
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0900
  time to fit residues: 9.2172
Evaluate side-chains
  82 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0060
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
H  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.158906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.130679 restraints weight = 4867.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.96
r_work: 0.3480 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4289  Z= 0.185
  Angle     :  0.657   9.121   5834  Z= 0.333
  Chirality :  0.046   0.230    641
  Planarity :  0.005   0.062    745
  Dihedral  :  5.803  36.123    617
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.48 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.55 (0.37), residues: 527
  helix: -1.57 (1.10), residues: 14
  sheet: -0.92 (0.33), residues: 232
  loop : -1.00 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARGD2 123 
 TYR   0.009   0.001   TYR L  49 
 PHE   0.025   0.002   PHE H 149 
 TRP   0.010   0.001   TRP I 233 
 HIS   0.003   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 4282)
  covalent geometry    : angle       0.63949 ( 5818)
  SS BOND              : bond        0.00366 (    5)
  SS BOND              : angle       0.86503 (   10)
  hydrogen bonds       : bond        0.02793 (  118)
  hydrogen bonds       : angle       6.28721 (  300)
  link_NAG-ASN         : bond        0.01068 (    2)
  link_NAG-ASN         : angle       4.63846 (    6)

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  222 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7259 (mm)
REVERT: I  276 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6795 (p90)
REVERT: L  197 THR cc_start: 0.8368 (m) cc_final: 0.8071 (p)
REVERT: H   53 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.8499 (p90)
REVERT: H   83 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7147 (mtt)
  outliers start: 11
  outliers final: 6
  residues processed: 81
  average time/residue: 0.0983
  time to fit residues: 9.4368
Evaluate side-chains
  85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  213 ILE
Chi-restraints excluded: chain I residue  222 ILE
Chi-restraints excluded: chain I residue  224 VAL
Chi-restraints excluded: chain I residue  267 THR
Chi-restraints excluded: chain I residue  276 HIS
Chi-restraints excluded: chain H residue   30 ASP
Chi-restraints excluded: chain H residue   53 TRP
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0470
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.164782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136653 restraints weight = 4883.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 1.96
r_work: 0.3533 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4289  Z= 0.131
  Angle     :  0.616   9.092   5834  Z= 0.312
  Chirality :  0.044   0.216    641
  Planarity :  0.005   0.061    745
  Dihedral  :  5.586  32.755    617
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 22.13 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.40 (0.37), residues: 527
  helix: -1.29 (1.13), residues: 14
  sheet: -0.74 (0.34), residues: 227
  loop : -1.00 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  26 
 TYR   0.014   0.001   TYR L 173 
 PHE   0.022   0.002   PHE H 149 
 TRP   0.010   0.001   TRP L 148 
 HIS   0.003   0.001   HIS H 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4282)
  covalent geometry    : angle       0.59910 ( 5818)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       0.72159 (   10)
  hydrogen bonds       : bond        0.02545 (  118)
  hydrogen bonds       : angle       6.07985 (  300)
  link_NAG-ASN         : bond        0.01090 (    2)
  link_NAG-ASN         : angle       4.53763 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1350.51 seconds
wall clock time: 23 minutes 44.32 seconds (1424.32 seconds total)