Starting phenix.real_space_refine
on Thu Mar  6 04:02:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b9y_44392/03_2025/9b9y_44392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b9y_44392/03_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_44392/03_2025/9b9y_44392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b9y_44392/03_2025/9b9y_44392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b9y_44392/03_2025/9b9y_44392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b9y_44392/03_2025/9b9y_44392.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.43, per 1000 atoms: 0.72
  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: 1.12
  Conformation dependent library (CDL) restraints added in 570.4 milliseconds
  

  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: 0.58
  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: 1.59

  Time building geometry restraints manager: 1.31 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.010
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.710
-------------------------------------------------------------------------------
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   4857  Z= 0.314
  Angle     :  1.158  69.442   6574  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (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
 TRP   0.010   0.001   TRP N  36 
 HIS   0.003   0.000   HIS R 219 
 PHE   0.031   0.002   PHE N 104 
 TYR   0.012   0.001   TYR N  94 
 ARG   0.006   0.000   ARG R 145 

*********************** 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  : 0.479 
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: 0.1313
  time to fit residues: 27.1284
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  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.093728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.073077 restraints weight = 9809.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.075879 restraints weight = 5007.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.077775 restraints weight = 3281.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4857  Z= 0.287
  Angle     :  0.590   8.480   6574  Z= 0.301
  Chirality :  0.043   0.168    750
  Planarity :  0.004   0.037    813
  Dihedral  :  4.901  38.652    670
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.38 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.34), residues: 597
  helix:  2.04 (0.28), residues: 320
  sheet:  1.88 (0.56), residues: 82
  loop : -1.43 (0.41), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 299 
 HIS   0.003   0.001   HIS R 219 
 PHE   0.015   0.001   PHE N  29 
 TYR   0.009   0.001   TYR R 215 
 ARG   0.006   0.001   ARG R 230 

*********************** 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
  139 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.531 
Fit side-chains
REVERT: R  230 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7885 (mmm-85)
REVERT: R  277 MET cc_start: 0.8382 (tmm) cc_final: 0.8085 (tmm)
REVERT: N   36 TRP cc_start: 0.9026 (m100) cc_final: 0.7402 (m100)
REVERT: N   82 MET cc_start: 0.8604 (pmm) cc_final: 0.8400 (pmm)
  outliers start: 9
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1280
  time to fit residues: 22.8246
Evaluate side-chains
  126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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 R residue  382 CYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   83 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0000
   chunk 42 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 = 0.3351 r_free = 0.3351 target = 0.096426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.075570 restraints weight = 9767.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.078561 restraints weight = 4879.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.080553 restraints weight = 3148.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4857  Z= 0.164
  Angle     :  0.542   7.992   6574  Z= 0.275
  Chirality :  0.041   0.150    750
  Planarity :  0.003   0.028    813
  Dihedral  :  4.474  33.791    670
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.93 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.34), residues: 597
  helix:  2.29 (0.28), residues: 320
  sheet:  1.80 (0.56), residues: 83
  loop : -1.34 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.007   0.001   PHE N  29 
 TYR   0.009   0.001   TYR R1109 
 ARG   0.004   0.000   ARG R 226 

*********************** 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
  143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 0.564 
Fit side-chains
REVERT: R  240 MET cc_start: 0.8721 (tmm) cc_final: 0.8013 (ttp)
REVERT: R  277 MET cc_start: 0.8307 (tmm) cc_final: 0.7951 (tmm)
REVERT: N   36 TRP cc_start: 0.9016 (m100) cc_final: 0.7643 (m100)
  outliers start: 10
  outliers final: 7
  residues processed: 136
  average time/residue: 0.1393
  time to fit residues: 25.0437
Evaluate side-chains
  126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  169 ILE
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   21 SER
Chi-restraints excluded: chain N residue   47 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.0070
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.096334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.075564 restraints weight = 9863.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.078547 restraints weight = 4926.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.080465 restraints weight = 3177.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4857  Z= 0.171
  Angle     :  0.570   9.655   6574  Z= 0.281
  Chirality :  0.042   0.160    750
  Planarity :  0.003   0.034    813
  Dihedral  :  4.215  32.598    670
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.52 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.34), residues: 597
  helix:  2.38 (0.28), residues: 321
  sheet:  1.95 (0.57), residues: 83
  loop : -1.24 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.007   0.001   PHE R1104 
 TYR   0.006   0.001   TYR R1109 
 ARG   0.006   0.000   ARG R 226 

*********************** 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
  136 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.541 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8272 (tmm) cc_final: 0.7910 (tmm)
REVERT: N   36 TRP cc_start: 0.9018 (m100) cc_final: 0.7627 (m100)
  outliers start: 12
  outliers final: 9
  residues processed: 127
  average time/residue: 0.1332
  time to fit residues: 22.6105
Evaluate side-chains
  129 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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 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   21 SER
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 10 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.096242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.075335 restraints weight = 10005.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.078293 restraints weight = 4951.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.080285 restraints weight = 3188.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4857  Z= 0.168
  Angle     :  0.583  10.575   6574  Z= 0.291
  Chirality :  0.042   0.171    750
  Planarity :  0.003   0.030    813
  Dihedral  :  4.028  32.084    670
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.31 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.34), residues: 597
  helix:  2.43 (0.28), residues: 320
  sheet:  2.02 (0.56), residues: 83
  loop : -1.25 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.005   0.001   PHE R 208 
 TYR   0.007   0.001   TYR R1109 
 ARG   0.005   0.000   ARG R 230 

*********************** 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
  143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.549 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8259 (tmm) cc_final: 0.7879 (tmm)
REVERT: R 1195 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8826 (t80)
REVERT: N   36 TRP cc_start: 0.9003 (m100) cc_final: 0.7639 (m100)
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1409
  time to fit residues: 24.6184
Evaluate side-chains
  133 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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 1195 PHE
Chi-restraints excluded: chain R residue  381 PHE
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   27 THR
Chi-restraints excluded: chain N residue   47 LEU
Chi-restraints excluded: chain N residue   48 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.091599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.070752 restraints weight = 10011.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.073526 restraints weight = 5055.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.075442 restraints weight = 3281.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4857  Z= 0.324
  Angle     :  0.647   8.814   6574  Z= 0.325
  Chirality :  0.044   0.182    750
  Planarity :  0.003   0.032    813
  Dihedral  :  3.982  31.790    670
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.09 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.34), residues: 597
  helix:  2.30 (0.28), residues: 325
  sheet:  1.82 (0.55), residues: 84
  loop : -1.35 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R1082 
 HIS   0.001   0.001   HIS R 219 
 PHE   0.010   0.001   PHE N  29 
 TYR   0.010   0.001   TYR R 215 
 ARG   0.009   0.001   ARG R 230 

*********************** 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
  141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.576 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8310 (tmm) cc_final: 0.7955 (tmm)
REVERT: R 1195 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.8902 (t80)
REVERT: N   36 TRP cc_start: 0.9122 (m100) cc_final: 0.7635 (m100)
REVERT: N   72 ASP cc_start: 0.8041 (t0) cc_final: 0.7642 (t0)
REVERT: N   82 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8392 (pmm)
  outliers start: 19
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1349
  time to fit residues: 23.0676
Evaluate side-chains
  136 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
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 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   17 SER
Chi-restraints excluded: chain N residue   21 SER
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.092969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.072509 restraints weight = 9829.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.075318 restraints weight = 4897.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.077306 restraints weight = 3159.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4857  Z= 0.221
  Angle     :  0.620   9.069   6574  Z= 0.310
  Chirality :  0.043   0.192    750
  Planarity :  0.003   0.030    813
  Dihedral  :  3.996  31.740    670
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.68 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.34), residues: 597
  helix:  2.44 (0.28), residues: 318
  sheet:  1.32 (0.51), residues: 100
  loop : -1.53 (0.43), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.009   0.001   PHE N 104 
 TYR   0.006   0.001   TYR R1109 
 ARG   0.004   0.000   ARG R 226 

*********************** 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
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.551 
Fit side-chains
REVERT: R  103 MET cc_start: 0.7473 (mtm) cc_final: 0.7211 (mtm)
REVERT: R  135 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9254 (mm)
REVERT: R  277 MET cc_start: 0.8256 (tmm) cc_final: 0.7892 (tmm)
REVERT: R 1195 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8884 (t80)
REVERT: R  371 MET cc_start: 0.7313 (tpt) cc_final: 0.7036 (tpp)
REVERT: N   36 TRP cc_start: 0.9099 (m100) cc_final: 0.7607 (m100)
REVERT: N   77 THR cc_start: 0.8569 (p) cc_final: 0.8345 (p)
REVERT: N   82 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8473 (pmm)
REVERT: N  117 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8554 (tp-100)
  outliers start: 19
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1321
  time to fit residues: 22.8204
Evaluate side-chains
  138 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
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 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   17 SER
Chi-restraints excluded: chain N residue   21 SER
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3292 r_free = 0.3292 target = 0.093234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.072318 restraints weight = 9938.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.075179 restraints weight = 4967.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.077117 restraints weight = 3219.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4857  Z= 0.238
  Angle     :  0.633   9.214   6574  Z= 0.316
  Chirality :  0.044   0.208    750
  Planarity :  0.003   0.028    813
  Dihedral  :  4.002  32.036    670
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 17.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.34), residues: 597
  helix:  2.44 (0.28), residues: 319
  sheet:  1.77 (0.56), residues: 82
  loop : -1.31 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP R 241 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.008   0.001   PHE N 104 
 TYR   0.007   0.001   TYR R 215 
 ARG   0.004   0.000   ARG R 230 

*********************** 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
  144 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.568 
Fit side-chains
REVERT: R  277 MET cc_start: 0.8264 (tmm) cc_final: 0.7892 (tmm)
REVERT: R 1195 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8925 (t80)
REVERT: R  371 MET cc_start: 0.7196 (tpt) cc_final: 0.6958 (tpp)
REVERT: N   36 TRP cc_start: 0.9124 (m100) cc_final: 0.7617 (m100)
REVERT: N   82 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8490 (pmm)
  outliers start: 21
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1354
  time to fit residues: 23.6754
Evaluate side-chains
  140 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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  382 CYS
Chi-restraints excluded: chain R residue  396 ILE
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   21 SER
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3282 r_free = 0.3282 target = 0.094210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.073262 restraints weight = 9685.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.076219 restraints weight = 4884.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.078230 restraints weight = 3147.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
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   0.033   4857  Z= 0.192
  Angle     :  0.641   8.950   6574  Z= 0.319
  Chirality :  0.043   0.210    750
  Planarity :  0.003   0.029    813
  Dihedral  :  4.023  32.055    670
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.34), residues: 597
  helix:  2.43 (0.28), residues: 319
  sheet:  1.85 (0.57), residues: 82
  loop : -1.28 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.023   0.001   PHE R 268 
 TYR   0.006   0.001   TYR R1109 
 ARG   0.005   0.000   ARG R 226 

*********************** 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
  151 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.516 
Fit side-chains
REVERT: R  135 LEU cc_start: 0.9508 (mm) cc_final: 0.9297 (mm)
REVERT: R  176 ASP cc_start: 0.8212 (t70) cc_final: 0.7363 (t0)
REVERT: R  277 MET cc_start: 0.8284 (tmm) cc_final: 0.7890 (tmm)
REVERT: R 1195 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8987 (t80)
REVERT: N    6 GLU cc_start: 0.8205 (pm20) cc_final: 0.7353 (pm20)
REVERT: N   36 TRP cc_start: 0.9076 (m100) cc_final: 0.7620 (m100)
REVERT: N   82 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8482 (pmm)
REVERT: N  114 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8448 (mp10)
REVERT: N  117 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8544 (tp-100)
  outliers start: 19
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1437
  time to fit residues: 26.3107
Evaluate side-chains
  142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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   17 SER
Chi-restraints excluded: chain N residue   21 SER
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   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 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 = 0.3289 r_free = 0.3289 target = 0.094576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.073805 restraints weight = 9562.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.076747 restraints weight = 4810.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.078657 restraints weight = 3094.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4857  Z= 0.196
  Angle     :  0.665   9.208   6574  Z= 0.328
  Chirality :  0.045   0.294    750
  Planarity :  0.003   0.032    813
  Dihedral  :  3.977  31.790    670
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.34), residues: 597
  helix:  2.39 (0.28), residues: 319
  sheet:  1.87 (0.57), residues: 82
  loop : -1.28 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.024   0.001   PHE R 268 
 TYR   0.011   0.001   TYR N  79 
 ARG   0.008   0.000   ARG R 230 

********************** 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
  146 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.500 
Fit side-chains
REVERT: R  135 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9288 (mm)
REVERT: R  176 ASP cc_start: 0.8195 (t70) cc_final: 0.7346 (t0)
REVERT: R  226 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7376 (ttt-90)
REVERT: R  277 MET cc_start: 0.8297 (tmm) cc_final: 0.7907 (tmm)
REVERT: R 1195 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.9026 (t80)
REVERT: R  360 LEU cc_start: 0.9405 (mm) cc_final: 0.9195 (mm)
REVERT: R  375 ILE cc_start: 0.9348 (mm) cc_final: 0.9055 (pt)
REVERT: N    6 GLU cc_start: 0.8262 (pm20) cc_final: 0.7622 (pm20)
REVERT: N   36 TRP cc_start: 0.9075 (m100) cc_final: 0.7602 (m100)
REVERT: N   82 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8482 (pmm)
REVERT: N  114 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8414 (mp10)
REVERT: N  117 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8483 (tp-100)
  outliers start: 19
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1464
  time to fit residues: 25.7417
Evaluate side-chains
  146 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
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   12 VAL
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   21 SER
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0270
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0000
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5844

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.095775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.074907 restraints weight = 9661.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.077902 restraints weight = 4869.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.079931 restraints weight = 3132.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4857  Z= 0.185
  Angle     :  0.651   8.877   6574  Z= 0.323
  Chirality :  0.044   0.227    750
  Planarity :  0.003   0.030    813
  Dihedral  :  3.919  31.706    670
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 18.07 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.35), residues: 597
  helix:  2.42 (0.28), residues: 319
  sheet:  1.94 (0.57), residues: 82
  loop : -1.31 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP R 299 
 HIS   0.002   0.000   HIS R 219 
 PHE   0.017   0.001   PHE R 268 
 TYR   0.022   0.001   TYR N  79 
 ARG   0.007   0.000   ARG R 226 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1752.80 seconds
wall clock time: 31 minutes 9.34 seconds (1869.34 seconds total)