Starting phenix.real_space_refine
on Wed Sep 17 05:07:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b9y_44392/09_2025/9b9y_44392.cif"
  }
  resolution = 3.5
  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=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     Cl      1      4.86       5
     C    3095      2.51       5
     N     786      2.21       5
     O     836      1.98       5
     F       3      1.80       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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4753
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "R"
      Number of atoms: 3775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3775
          Classifications: {'peptide': 478}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 464}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "N"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 942
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "R"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'7DY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.40, per 1000 atoms: 0.29
  Number of scatterers: 4753
  At special positions: 0
  Unit cell: (65.27, 88.81, 116.63, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      32     16.00
     F       3      9.00
     O     836      8.00
     N     786      7.00
     C    3095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 257 " - pdb=" SG  CYS R 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  95 " 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
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 190.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1116

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 5 sheets defined
      61.1% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'R' and resid 104 through 109
      removed outlier: 3.860A  pdb=" N   PHE R 108 " --> pdb=" O   ASP R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 144
    Processing helix  chain 'R' and resid 144 through 149
    Processing helix  chain 'R' and resid 150 through 152
      No H-bonds generated for 'chain 'R' and resid 150 through 152'
    Processing helix  chain 'R' and resid 153 through 176
      removed outlier: 3.910A  pdb=" N   GLY R 157 " --> pdb=" O   TYR R 153 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER R 167 " --> pdb=" O   ASP R 163 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE R 169 " --> pdb=" O   LEU R 165 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE R 170 " --> pdb=" O   GLY R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 220
    Processing helix  chain 'R' and resid 220 through 228
      removed outlier: 4.667A  pdb=" N   LYS R 225 " --> pdb=" O   PRO R 221 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   ARG R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   VAL R 228 " --> pdb=" O   TYR R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 250
    Processing helix  chain 'R' and resid 251 through 254
    Processing helix  chain 'R' and resid 256 through 261
      removed outlier: 3.529A  pdb=" N   LEU R 260 " --> pdb=" O   ASN R 256 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 1005
      removed outlier: 3.610A  pdb=" N   LEU R 276 " --> pdb=" O   ASP R 272 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE R1002 " --> pdb=" O   TRP R 299 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER R1005 " --> pdb=" O   GLY R1001 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1006 through 1007
      No H-bonds generated for 'chain 'R' and resid 1006 through 1007'
    Processing helix  chain 'R' and resid 1008 through 1012
      removed outlier: 3.657A  pdb=" N   TYR R1011 " --> pdb=" O   ASN R1008 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1015 through 1027
    Processing helix  chain 'R' and resid 1047 through 1059
    Processing helix  chain 'R' and resid 1076 through 1090
    Processing helix  chain 'R' and resid 1101 through 1112
    Processing helix  chain 'R' and resid 1125 through 1134
      removed outlier: 3.585A  pdb=" N   LEU R1134 " --> pdb=" O   GLU R1130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1145 through 1150
      removed outlier: 3.834A  pdb=" N   ILE R1150 " --> pdb=" O   LEU R1146 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1162 through 1177
    Processing helix  chain 'R' and resid 1181 through 1195
    Processing helix  chain 'R' and resid 1196 through 368
      removed outlier: 3.779A  pdb=" N   ARG R 336 " --> pdb=" O   SER R1196 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 372 through 383
    Processing helix  chain 'R' and resid 384 through 401
      Proline residue:  R 394  - end of helix
      removed outlier: 3.859A  pdb=" N   TYR R 397 " --> pdb=" O   ASN R 393 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA R 398 " --> pdb=" O   PRO R 394 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 401 through 412
    Processing sheet with id=AA1, first strand: chain 'R' and resid 1093 through 1096
      removed outlier: 8.596A  pdb=" N   LYS R1094 " --> pdb=" O   MET R1067 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE R1069 " --> pdb=" O   LYS R1094 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ILE R1096 " --> pdb=" O   PHE R1069 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE R1071 " --> pdb=" O   ILE R1096 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL R1033 " --> pdb=" O   ARG R1068 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ILE R1070 " --> pdb=" O   VAL R1033 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE R1035 " --> pdb=" O   ILE R1070 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ILE R1072 " --> pdb=" O   PHE R1035 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   PHE R1037 " --> pdb=" O   ILE R1072 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR R1034 " --> pdb=" O   PHE R1114 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   ILE R1116 " --> pdb=" O   THR R1034 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET R1036 " --> pdb=" O   ILE R1116 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL R1115 " --> pdb=" O   ILE R1139 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   SER R1141 " --> pdb=" O   VAL R1115 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE R1117 " --> pdb=" O   SER R1141 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   VAL R1158 " --> pdb=" O   PRO R1138 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA R1140 " --> pdb=" O   VAL R1158 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'N' and resid 12 through 13
      removed outlier: 6.814A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 121 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'N' and resid 58 through 59
      removed outlier: 6.687A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   GLY N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   MET N  34 " --> pdb=" O   GLY N  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'N' and resid 58 through 59
      removed outlier: 6.687A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   GLY N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   MET N  34 " --> pdb=" O   GLY N  50 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    864 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: 0.90

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 742
        1.31 -     1.43: 1334
        1.43 -     1.56: 2730
        1.56 -     1.69: 0
        1.69 -     1.82: 51
  Bond restraints: 4857
  Sorted by residual:
  bond pdb=" CBE 7DY R1201 "
       pdb=" NAI 7DY R1201 "
    ideal  model  delta    sigma   weight residual
    1.152  1.455 -0.303 2.00e-02 2.50e+03 2.29e+02
  bond pdb=" CAQ 7DY R1201 "
       pdb=" NAG 7DY R1201 "
    ideal  model  delta    sigma   weight residual
    1.343  1.457 -0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" CAX 7DY R1201 "
       pdb=" CBE 7DY R1201 "
    ideal  model  delta    sigma   weight residual
    1.428  1.524 -0.096 2.00e-02 2.50e+03 2.32e+01
  bond pdb=" CBD 7DY R1201 "
       pdb=" OAE 7DY R1201 "
    ideal  model  delta    sigma   weight residual
    1.327  1.413 -0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" CBC 7DY R1201 "
       pdb="CLAA 7DY R1201 "
    ideal  model  delta    sigma   weight residual
    1.736  1.784 -0.048 2.00e-02 2.50e+03 5.78e+00
  ... (remaining 4852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.89: 6573
       13.89 -    27.78: 0
       27.78 -    41.67: 0
       41.67 -    55.55: 0
       55.55 -    69.44: 1
  Bond angle restraints: 6574
  Sorted by residual:
  angle pdb=" CAX 7DY R1201 "
        pdb=" CBE 7DY R1201 "
        pdb=" NAI 7DY R1201 "
      ideal   model   delta    sigma   weight residual
     180.00  110.56   69.44 3.00e+00 1.11e-01 5.36e+02
  angle pdb=" N   VAL N  48 "
        pdb=" CA  VAL N  48 "
        pdb=" C   VAL N  48 "
      ideal   model   delta    sigma   weight residual
     110.72  115.30   -4.58 1.01e+00 9.80e-01 2.05e+01
  angle pdb=" CB  MET R1193 "
        pdb=" CG  MET R1193 "
        pdb=" SD  MET R1193 "
      ideal   model   delta    sigma   weight residual
     112.70  124.13  -11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CAQ 7DY R1201 "
        pdb=" CAP 7DY R1201 "
        pdb=" OAE 7DY R1201 "
      ideal   model   delta    sigma   weight residual
     101.99  113.29  -11.30 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" N   TYR R1109 "
        pdb=" CA  TYR R1109 "
        pdb=" C   TYR R1109 "
      ideal   model   delta    sigma   weight residual
     111.28  108.05    3.23 1.09e+00 8.42e-01 8.77e+00
  ... (remaining 6569 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2570
       17.95 -    35.90: 249
       35.90 -    53.85: 45
       53.85 -    71.79: 7
       71.79 -    89.74: 2
  Dihedral angle restraints: 2873
    sinusoidal: 1135
      harmonic: 1738
  Sorted by residual:
  dihedral pdb=" CB  CYS R 257 "
           pdb=" SG  CYS R 257 "
           pdb=" SG  CYS R 264 "
           pdb=" CB  CYS R 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.51   44.51     1      1.00e+01 1.00e-02 2.75e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  95 "
           pdb=" CB  CYS N  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.69   37.31     1      1.00e+01 1.00e-02 1.96e+01
  dihedral pdb=" C   VAL N  48 "
           pdb=" N   VAL N  48 "
           pdb=" CA  VAL N  48 "
           pdb=" CB  VAL N  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.44    9.44     0      2.50e+00 1.60e-01 1.43e+01
  ... (remaining 2870 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 652
       0.069 -    0.137: 94
       0.137 -    0.206: 2
       0.206 -    0.274: 1
       0.274 -    0.343: 1
  Chirality restraints: 750
  Sorted by residual:
  chirality pdb=" CB  ILE N  28 "
            pdb=" CA  ILE N  28 "
            pdb=" CG1 ILE N  28 "
            pdb=" CG2 ILE N  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CA  VAL N  48 "
            pdb=" N   VAL N  48 "
            pdb=" C   VAL N  48 "
            pdb=" CB  VAL N  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.21    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  SER R1111 "
            pdb=" N   SER R1111 "
            pdb=" C   SER R1111 "
            pdb=" CB  SER R1111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 747 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAJ 7DY R1201 "    0.156 2.00e-02 2.50e+03   2.59e-01 1.51e+03
        pdb=" CAM 7DY R1201 "    0.051 2.00e-02 2.50e+03
        pdb=" CAR 7DY R1201 "   -0.116 2.00e-02 2.50e+03
        pdb=" CAS 7DY R1201 "    0.103 2.00e-02 2.50e+03
        pdb=" CAX 7DY R1201 "   -0.215 2.00e-02 2.50e+03
        pdb=" CAY 7DY R1201 "    0.001 2.00e-02 2.50e+03
        pdb=" CAZ 7DY R1201 "   -0.158 2.00e-02 2.50e+03
        pdb=" CBE 7DY R1201 "   -0.393 2.00e-02 2.50e+03
        pdb=" NAI 7DY R1201 "    0.573 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 112 "   -0.033 5.00e-02 4.00e+02   5.08e-02 4.12e+00
        pdb=" N   PRO R 113 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO R 113 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 113 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE N 104 "    0.014 2.00e-02 2.50e+03   1.39e-02 3.38e+00
        pdb=" CG  PHE N 104 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE N 104 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE N 104 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE N 104 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE N 104 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE N 104 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1284
        2.81 -     3.33: 4582
        3.33 -     3.86: 7769
        3.86 -     4.38: 8615
        4.38 -     4.90: 15216
  Nonbonded interactions: 37466
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 265 "
            pdb=" O   PHE R 268 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   ARG R 148 "
            pdb=" NH1 ARG R 230 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NH1 ARG R 214 "
            pdb=" OD1 ASP R 338 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OD1 ASP R 272 "
            pdb=" OG1 THR R 274 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   GLY R 166 "
            pdb=" NAI 7DY R1201 "
     model   vdw
     2.345 3.120
  ... (remaining 37461 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.830
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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   0.303   4859  Z= 0.306
  Angle     :  1.158  69.442   6578  Z= 0.479
  Chirality :  0.048   0.343    750
  Planarity :  0.010   0.259    813
  Dihedral  : 14.200  89.743   1751
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.65 (0.33), residues: 597
  helix:  1.28 (0.27), residues: 312
  sheet:  1.76 (0.58), residues: 81
  loop : -1.49 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 145 
 TYR   0.012   0.001   TYR N  94 
 PHE   0.031   0.002   PHE N 104 
 TRP   0.010   0.001   TRP N  36 
 HIS   0.003   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 4857)
  covalent geometry    : angle       1.15762 ( 6574)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.18744 (    4)
  hydrogen bonds       : bond        0.14450 (  287)
  hydrogen bonds       : angle       5.55682 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.196 
Fit side-chains
REVERT: R  135 LEU cc_start: 0.9409 (mm) cc_final: 0.9141 (mm)
REVERT: R  139 CYS cc_start: 0.8651 (m) cc_final: 0.8363 (m)
REVERT: R  256 ASN cc_start: 0.9270 (p0) cc_final: 0.8637 (p0)
REVERT: R  277 MET cc_start: 0.8348 (tmm) cc_final: 0.8001 (tmm)
REVERT: R 1168 ASN cc_start: 0.8852 (m110) cc_final: 0.8514 (m110)
REVERT: R 1187 ASN cc_start: 0.8991 (m-40) cc_final: 0.8714 (m-40)
REVERT: N   36 TRP cc_start: 0.9101 (m100) cc_final: 0.8123 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0640
  time to fit residues: 13.3573
Evaluate side-chains
  129 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
R 134 ASN
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** 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 = 0.3362 r_free = 0.3362 target = 0.097246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.076341 restraints weight = 9701.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.079263 restraints weight = 4960.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.081231 restraints weight = 3235.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.082437 restraints weight = 2447.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.083391 restraints weight = 2052.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4859  Z= 0.125
  Angle     :  0.555   8.311   6578  Z= 0.281
  Chirality :  0.042   0.147    750
  Planarity :  0.003   0.037    813
  Dihedral  :  4.953  42.275    670
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.79 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.47 (0.34), residues: 597
  helix:  2.06 (0.27), residues: 320
  sheet:  1.98 (0.57), residues: 80
  loop : -1.39 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 230 
 TYR   0.009   0.001   TYR N 106 
 PHE   0.013   0.001   PHE N 104 
 TRP   0.007   0.001   TRP R 299 
 HIS   0.003   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4857)
  covalent geometry    : angle       0.55467 ( 6574)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.72521 (    4)
  hydrogen bonds       : bond        0.03853 (  287)
  hydrogen bonds       : angle       3.89054 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.236 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8348 (tmm) cc_final: 0.7998 (tmm)
REVERT: N   36 TRP cc_start: 0.8922 (m100) cc_final: 0.7467 (m100)
REVERT: N   82 MET cc_start: 0.8523 (pmm) cc_final: 0.8174 (pmm)
  outliers start: 7
  outliers final: 6
  residues processed: 130
  average time/residue: 0.0653
  time to fit residues: 11.3277
Evaluate side-chains
  123 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   47 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.072215 restraints weight = 9915.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.075045 restraints weight = 5005.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076988 restraints weight = 3241.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.078247 restraints weight = 2446.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.079088 restraints weight = 2035.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4859  Z= 0.199
  Angle     :  0.592   8.185   6578  Z= 0.302
  Chirality :  0.043   0.155    750
  Planarity :  0.004   0.035    813
  Dihedral  :  4.367  33.410    670
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.54 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.57 (0.34), residues: 597
  helix:  2.12 (0.28), residues: 327
  sheet:  1.81 (0.57), residues: 83
  loop : -1.36 (0.43), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 230 
 TYR   0.009   0.001   TYR R1109 
 PHE   0.014   0.001   PHE N  29 
 TRP   0.003   0.001   TRP R1082 
 HIS   0.003   0.001   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4857)
  covalent geometry    : angle       0.59150 ( 6574)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       1.22659 (    4)
  hydrogen bonds       : bond        0.03961 (  287)
  hydrogen bonds       : angle       3.87696 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.207 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8315 (tmm) cc_final: 0.7989 (tmm)
REVERT: N   36 TRP cc_start: 0.9136 (m100) cc_final: 0.7732 (m100)
  outliers start: 14
  outliers final: 10
  residues processed: 130
  average time/residue: 0.0608
  time to fit residues: 10.7640
Evaluate side-chains
  123 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  382 CYS
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.094437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.073919 restraints weight = 9846.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.076828 restraints weight = 4987.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.078756 restraints weight = 3234.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.080082 restraints weight = 2441.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.080859 restraints weight = 2021.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4859  Z= 0.123
  Angle     :  0.569   8.238   6578  Z= 0.286
  Chirality :  0.043   0.206    750
  Planarity :  0.003   0.027    813
  Dihedral  :  3.984  32.577    670
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.72 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.80 (0.34), residues: 597
  helix:  2.33 (0.28), residues: 321
  sheet:  1.93 (0.56), residues: 83
  loop : -1.22 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 226 
 TYR   0.006   0.001   TYR R1109 
 PHE   0.007   0.001   PHE N  67 
 TRP   0.004   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4857)
  covalent geometry    : angle       0.56924 ( 6574)
  SS BOND              : bond        0.00102 (    2)
  SS BOND              : angle       0.67011 (    4)
  hydrogen bonds       : bond        0.03666 (  287)
  hydrogen bonds       : angle       3.74372 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.119 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8249 (tmm) cc_final: 0.7884 (tmm)
REVERT: N   36 TRP cc_start: 0.9059 (m100) cc_final: 0.7736 (m100)
  outliers start: 13
  outliers final: 10
  residues processed: 126
  average time/residue: 0.0606
  time to fit residues: 10.2467
Evaluate side-chains
  125 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.093772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.073174 restraints weight = 9898.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.076081 restraints weight = 4958.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.078042 restraints weight = 3209.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.079380 restraints weight = 2411.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.080163 restraints weight = 1992.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4859  Z= 0.144
  Angle     :  0.581   8.382   6578  Z= 0.293
  Chirality :  0.042   0.179    750
  Planarity :  0.003   0.032    813
  Dihedral  :  3.900  32.976    670
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.70 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.85 (0.34), residues: 597
  helix:  2.37 (0.28), residues: 321
  sheet:  1.96 (0.56), residues: 83
  loop : -1.19 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 226 
 TYR   0.007   0.001   TYR R1109 
 PHE   0.007   0.001   PHE N  29 
 TRP   0.003   0.001   TRP R 241 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4857)
  covalent geometry    : angle       0.58075 ( 6574)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.68712 (    4)
  hydrogen bonds       : bond        0.03682 (  287)
  hydrogen bonds       : angle       3.76188 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: R  277 MET cc_start: 0.8238 (tmm) cc_final: 0.7892 (tmm)
REVERT: N   36 TRP cc_start: 0.9082 (m100) cc_final: 0.7733 (m100)
REVERT: N   82 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8404 (pmm)
  outliers start: 19
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0569
  time to fit residues: 9.8228
Evaluate side-chains
  132 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue 1107 GLU
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  382 CYS
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.094717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.073941 restraints weight = 9909.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.076895 restraints weight = 4954.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.078889 restraints weight = 3210.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.080231 restraints weight = 2407.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.080939 restraints weight = 1983.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4859  Z= 0.127
  Angle     :  0.587   8.642   6578  Z= 0.292
  Chirality :  0.043   0.188    750
  Planarity :  0.003   0.031    813
  Dihedral  :  3.841  32.747    670
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.07 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.79 (0.34), residues: 597
  helix:  2.37 (0.28), residues: 321
  sheet:  1.47 (0.51), residues: 100
  loop : -1.36 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 226 
 TYR   0.005   0.001   TYR R 215 
 PHE   0.005   0.001   PHE R 208 
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4857)
  covalent geometry    : angle       0.58663 ( 6574)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.55760 (    4)
  hydrogen bonds       : bond        0.03603 (  287)
  hydrogen bonds       : angle       3.71584 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.186 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8240 (tmm) cc_final: 0.7866 (tmm)
REVERT: R 1195 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8879 (t80)
REVERT: N   36 TRP cc_start: 0.9054 (m100) cc_final: 0.7723 (m100)
REVERT: N   72 ASP cc_start: 0.7993 (t0) cc_final: 0.7753 (t0)
REVERT: N   82 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8388 (pmm)
  outliers start: 20
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0618
  time to fit residues: 10.8914
Evaluate side-chains
  133 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue 1158 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  382 CYS
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.095227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.074550 restraints weight = 9845.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.077461 restraints weight = 4982.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.079452 restraints weight = 3225.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.080751 restraints weight = 2422.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.081539 restraints weight = 2006.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4859  Z= 0.124
  Angle     :  0.602   8.787   6578  Z= 0.302
  Chirality :  0.043   0.200    750
  Planarity :  0.003   0.040    813
  Dihedral  :  3.864  32.356    670
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.25 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.34), residues: 597
  helix:  2.35 (0.28), residues: 321
  sheet:  1.53 (0.51), residues: 100
  loop : -1.39 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 230 
 TYR   0.007   0.001   TYR R1109 
 PHE   0.006   0.001   PHE N  29 
 TRP   0.003   0.000   TRP R 299 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4857)
  covalent geometry    : angle       0.60218 ( 6574)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       0.56359 (    4)
  hydrogen bonds       : bond        0.03595 (  287)
  hydrogen bonds       : angle       3.75917 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.189 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8235 (tmm) cc_final: 0.7850 (tmm)
REVERT: R 1195 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8900 (t80)
REVERT: R  371 MET cc_start: 0.7062 (tpt) cc_final: 0.6774 (tpp)
REVERT: N   36 TRP cc_start: 0.9059 (m100) cc_final: 0.7619 (m100)
REVERT: N   82 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8370 (pmm)
REVERT: N  100 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8569 (mp)
REVERT: N  117 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8571 (tp-100)
  outliers start: 18
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0599
  time to fit residues: 10.5933
Evaluate side-chains
  137 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  264 CYS
Chi-restraints excluded: chain R residue 1158 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.095064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.074270 restraints weight = 9855.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.077179 restraints weight = 4991.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.079182 restraints weight = 3236.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.080491 restraints weight = 2426.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.081208 restraints weight = 2007.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4859  Z= 0.129
  Angle     :  0.631   9.183   6578  Z= 0.315
  Chirality :  0.044   0.206    750
  Planarity :  0.003   0.042    813
  Dihedral  :  3.842  32.088    670
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.65 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.34), residues: 597
  helix:  2.31 (0.28), residues: 321
  sheet:  2.05 (0.57), residues: 83
  loop : -1.19 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 230 
 TYR   0.006   0.001   TYR R1109 
 PHE   0.009   0.001   PHE R 268 
 TRP   0.003   0.000   TRP R 299 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4857)
  covalent geometry    : angle       0.63102 ( 6574)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       0.59656 (    4)
  hydrogen bonds       : bond        0.03622 (  287)
  hydrogen bonds       : angle       3.79305 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.193 
Fit side-chains
REVERT: R  135 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9233 (mm)
REVERT: R  176 ASP cc_start: 0.8183 (t70) cc_final: 0.7801 (t0)
REVERT: R  277 MET cc_start: 0.8230 (tmm) cc_final: 0.7846 (tmm)
REVERT: R 1195 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8935 (t80)
REVERT: R  371 MET cc_start: 0.7130 (tpt) cc_final: 0.6820 (tpp)
REVERT: N   36 TRP cc_start: 0.9063 (m100) cc_final: 0.7620 (m100)
REVERT: N   72 ASP cc_start: 0.7958 (t0) cc_final: 0.7665 (t0)
REVERT: N   82 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8360 (pmm)
REVERT: N  100 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8587 (mp)
  outliers start: 16
  outliers final: 12
  residues processed: 134
  average time/residue: 0.0638
  time to fit residues: 11.4077
Evaluate side-chains
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  264 CYS
Chi-restraints excluded: chain R residue 1158 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.096173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.075384 restraints weight = 9786.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.078289 restraints weight = 4918.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.080312 restraints weight = 3187.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.081547 restraints weight = 2399.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.082439 restraints weight = 2002.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4859  Z= 0.128
  Angle     :  0.637   8.628   6578  Z= 0.320
  Chirality :  0.044   0.222    750
  Planarity :  0.003   0.030    813
  Dihedral  :  3.878  31.984    670
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 19.25 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.85 (0.35), residues: 597
  helix:  2.41 (0.28), residues: 319
  sheet:  2.03 (0.58), residues: 81
  loop : -1.23 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 230 
 TYR   0.010   0.001   TYR N  79 
 PHE   0.008   0.001   PHE R 268 
 TRP   0.003   0.000   TRP R 299 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4857)
  covalent geometry    : angle       0.63655 ( 6574)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.70265 (    4)
  hydrogen bonds       : bond        0.03560 (  287)
  hydrogen bonds       : angle       3.78724 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: R  176 ASP cc_start: 0.8239 (t70) cc_final: 0.7395 (t0)
REVERT: R  277 MET cc_start: 0.8218 (tmm) cc_final: 0.7835 (tmm)
REVERT: R 1195 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8963 (t80)
REVERT: N    6 GLU cc_start: 0.7828 (mp0) cc_final: 0.7202 (pm20)
REVERT: N   36 TRP cc_start: 0.9059 (m100) cc_final: 0.7616 (m100)
REVERT: N   63 VAL cc_start: 0.9408 (t) cc_final: 0.9122 (p)
REVERT: N   82 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8370 (pmm)
REVERT: N  100 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8628 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 135
  average time/residue: 0.0613
  time to fit residues: 11.0090
Evaluate side-chains
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  264 CYS
Chi-restraints excluded: chain R residue 1158 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 4 optimal weight:    0.3980
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.094699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.074029 restraints weight = 9681.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.076964 restraints weight = 4886.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.078864 restraints weight = 3157.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.080299 restraints weight = 2384.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.081123 restraints weight = 1956.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4859  Z= 0.144
  Angle     :  0.663   9.026   6578  Z= 0.330
  Chirality :  0.045   0.218    750
  Planarity :  0.003   0.032    813
  Dihedral  :  3.902  31.946    670
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.04 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.35), residues: 597
  helix:  2.40 (0.28), residues: 319
  sheet:  1.99 (0.58), residues: 81
  loop : -1.28 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 226 
 TYR   0.019   0.001   TYR N  79 
 PHE   0.009   0.001   PHE R 268 
 TRP   0.002   0.001   TRP R 279 
 HIS   0.001   0.000   HIS R 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4857)
  covalent geometry    : angle       0.66313 ( 6574)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.79963 (    4)
  hydrogen bonds       : bond        0.03669 (  287)
  hydrogen bonds       : angle       3.81823 (  864)

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

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

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1194 Ramachandran restraints generated.
    597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.184 
Fit side-chains
REVERT: R  176 ASP cc_start: 0.8198 (t70) cc_final: 0.7351 (t0)
REVERT: R  277 MET cc_start: 0.8240 (tmm) cc_final: 0.7841 (tmm)
REVERT: R 1195 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.9025 (t80)
REVERT: R  375 ILE cc_start: 0.9341 (mm) cc_final: 0.9062 (pt)
REVERT: N   36 TRP cc_start: 0.9090 (m100) cc_final: 0.7630 (m100)
REVERT: N   82 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8389 (pmm)
REVERT: N  100 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8591 (mp)
REVERT: N  114 GLN cc_start: 0.8626 (mp10) cc_final: 0.8372 (mp10)
  outliers start: 16
  outliers final: 12
  residues processed: 134
  average time/residue: 0.0636
  time to fit residues: 11.2089
Evaluate side-chains
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  227 ILE
Chi-restraints excluded: chain R residue  253 LEU
Chi-restraints excluded: chain R residue  264 CYS
Chi-restraints excluded: chain R residue 1158 VAL
Chi-restraints excluded: chain R residue 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   82 MET
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 116 GLN
** R 389 ASN ** 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 = 0.3298 r_free = 0.3298 target = 0.095093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.074331 restraints weight = 9660.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.077316 restraints weight = 4870.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.079343 restraints weight = 3143.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.080697 restraints weight = 2349.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.081543 restraints weight = 1931.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4859  Z= 0.136
  Angle     :  0.665   8.781   6578  Z= 0.333
  Chirality :  0.044   0.222    750
  Planarity :  0.003   0.035    813
  Dihedral  :  3.932  31.906    670
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.43 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.78 (0.35), residues: 597
  helix:  2.39 (0.28), residues: 319
  sheet:  1.92 (0.58), residues: 81
  loop : -1.29 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 226 
 TYR   0.006   0.001   TYR R 397 
 PHE   0.008   0.001   PHE N  29 
 TRP   0.004   0.001   TRP N 112 
 HIS   0.002   0.000   HIS R 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4857)
  covalent geometry    : angle       0.66454 ( 6574)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.71124 (    4)
  hydrogen bonds       : bond        0.03596 (  287)
  hydrogen bonds       : angle       3.81725 (  864)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1001.88 seconds
wall clock time: 17 minutes 58.96 seconds (1078.96 seconds total)