Starting phenix.real_space_refine
on Fri Mar 14 02:11:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tyi_20583/03_2025/6tyi_20583.cif"
  }
  resolution = 3.3
  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=   0.008 sd=   0.148
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      36      5.16       5
     C    5894      2.51       5
     N    1567      2.21       5
     O    1683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9184
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1702
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 221}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1704
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 4, 'TRANS': 220}
    Chain: "C"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1712
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
    Chain: "D"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1712
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
    Chain: "E"
      Number of atoms: 1696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1696
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 4, 'TRANS': 219}
    Chain: "Y"
      Number of atoms: 236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 236
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 2, 'TRANS': 28}
    Chain: "Z"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 224
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 2, 'TRANS': 26}
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'PEV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.10, per 1000 atoms: 0.66
  Number of scatterers: 9184
  At special positions: 0
  Unit cell: (84.8, 84.8, 121.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       4     15.00
     O    1683      8.00
     N    1567      7.00
     C    5894      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      86.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 21 through 63
      removed outlier: 4.514A  pdb=" N   VAL A  46 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLU A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 103 through 128
    Processing helix  chain 'A' and resid 129 through 159
      removed outlier: 3.913A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 176 through 233
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'B' and resid 11 through 18
      removed outlier: 3.597A  pdb=" N   HIS B  18 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 63
    Processing helix  chain 'B' and resid 67 through 75
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    Processing helix  chain 'B' and resid 82 through 98
      removed outlier: 4.075A  pdb=" N   LEU B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 127
      removed outlier: 3.694A  pdb=" N   ILE B 107 " --> pdb=" O   ASP B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 162
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 170 through 233
      removed outlier: 3.754A  pdb=" N   THR B 181 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      Proline residue:  B 190  - end of helix
    Processing helix  chain 'C' and resid 20 through 63
    Processing helix  chain 'C' and resid 67 through 75
    Processing helix  chain 'C' and resid 76 through 78
      No H-bonds generated for 'chain 'C' and resid 76 through 78'
    Processing helix  chain 'C' and resid 82 through 98
    Processing helix  chain 'C' and resid 103 through 127
    Processing helix  chain 'C' and resid 129 through 163
      Proline residue:  C 141  - end of helix
    Processing helix  chain 'C' and resid 170 through 232
      removed outlier: 3.567A  pdb=" N   ILE C 174 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      Proline residue:  C 190  - end of helix
    Processing helix  chain 'D' and resid 11 through 16
    Processing helix  chain 'D' and resid 21 through 63
    Processing helix  chain 'D' and resid 67 through 75
    Processing helix  chain 'D' and resid 82 through 98
    Processing helix  chain 'D' and resid 103 through 128
    Processing helix  chain 'D' and resid 129 through 161
      removed outlier: 4.063A  pdb=" N   LEU D 133 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      Proline residue:  D 141  - end of helix
    Processing helix  chain 'D' and resid 170 through 233
      removed outlier: 3.666A  pdb=" N   ALA D 180 " --> pdb=" O   GLU D 176 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR D 181 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
      Proline residue:  D 190  - end of helix
    Processing helix  chain 'E' and resid 12 through 16
      removed outlier: 3.662A  pdb=" N   MET E  15 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR E  16 " --> pdb=" O   TRP E  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 12 through 16'
    Processing helix  chain 'E' and resid 23 through 63
      removed outlier: 4.278A  pdb=" N   GLY E  29 " --> pdb=" O   CYS E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 75
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 82 through 98
    Processing helix  chain 'E' and resid 103 through 127
    Processing helix  chain 'E' and resid 129 through 162
      Proline residue:  E 141  - end of helix
      removed outlier: 3.813A  pdb=" N   ALA E 160 " --> pdb=" O   PHE E 156 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN E 161 " --> pdb=" O   ILE E 157 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   THR E 162 " --> pdb=" O   GLY E 158 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 233
      removed outlier: 3.658A  pdb=" N   ILE E 174 " --> pdb=" O   VAL E 170 " (cutoff:3.500A)
      Proline residue:  E 190  - end of helix
    Processing helix  chain 'Y' and resid 20 through 37
      removed outlier: 3.962A  pdb=" N   VAL Y  26 " --> pdb=" O   PRO Y  22 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   MET Y  27 " --> pdb=" O   PHE Y  23 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL Y  29 " --> pdb=" O   ASP Y  25 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU Y  31 " --> pdb=" O   MET Y  27 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   PHE Y  34 " --> pdb=" O   LEU Y  30 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 38 through 42
    Processing helix  chain 'Z' and resid 23 through 36
      removed outlier: 3.735A  pdb=" N   MET Z  27 " --> pdb=" O   PHE Z  23 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE Z  32 " --> pdb=" O   LEU Z  28 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL Z  36 " --> pdb=" O   ILE Z  32 " (cutoff:3.500A)

    816 hydrogen bonds defined for protein.
    2442 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: 2.55

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1524
        1.30 -     1.43: 2284
        1.43 -     1.55: 5412
        1.55 -     1.68: 30
        1.68 -     1.80: 67
  Bond restraints: 9317
  Sorted by residual:
  bond pdb=" C11 PGT A 301 "
       pdb=" O3  PGT A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.431 -0.104 2.00e-02 2.50e+03 2.69e+01
  bond pdb=" C31 PGT A 301 "
       pdb=" O2  PGT A 301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.404 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C31 PEV C 301 "
       pdb=" O2  PEV C 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.403 -0.073 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C31 PEV E 301 "
       pdb=" O2  PEV E 301 "
    ideal  model  delta    sigma   weight residual
    1.330  1.402 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C11 PEV C 301 "
       pdb=" O3  PEV C 301 "
    ideal  model  delta    sigma   weight residual
    1.335  1.398 -0.063 2.00e-02 2.50e+03 9.83e+00
  ... (remaining 9312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.73: 12415
        3.73 -     7.47: 140
        7.47 -    11.20: 9
       11.20 -    14.93: 0
       14.93 -    18.66: 6
  Bond angle restraints: 12570
  Sorted by residual:
  angle pdb=" O3P PGT A 301 "
        pdb=" P   PGT A 301 "
        pdb=" O4P PGT A 301 "
      ideal   model   delta    sigma   weight residual
      92.82  111.48  -18.66 3.00e+00 1.11e-01 3.87e+01
  angle pdb=" O1P PEV C 301 "
        pdb=" P   PEV C 301 "
        pdb=" O2P PEV C 301 "
      ideal   model   delta    sigma   weight residual
     119.37  100.88   18.49 3.00e+00 1.11e-01 3.80e+01
  angle pdb=" O3P PEV C 301 "
        pdb=" P   PEV C 301 "
        pdb=" O4P PEV C 301 "
      ideal   model   delta    sigma   weight residual
      93.57  111.90  -18.33 3.00e+00 1.11e-01 3.73e+01
  angle pdb=" O1P PGT A 301 "
        pdb=" P   PGT A 301 "
        pdb=" O2P PGT A 301 "
      ideal   model   delta    sigma   weight residual
     119.10  100.80   18.30 3.00e+00 1.11e-01 3.72e+01
  angle pdb=" O3P PEV E 301 "
        pdb=" P   PEV E 301 "
        pdb=" O4P PEV E 301 "
      ideal   model   delta    sigma   weight residual
      93.57  111.77  -18.20 3.00e+00 1.11e-01 3.68e+01
  ... (remaining 12565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.60: 5232
       25.60 -    51.19: 322
       51.19 -    76.79: 49
       76.79 -   102.39: 6
      102.39 -   127.98: 2
  Dihedral angle restraints: 5611
    sinusoidal: 2239
      harmonic: 3372
  Sorted by residual:
  dihedral pdb=" CA  ALA A  19 "
           pdb=" C   ALA A  19 "
           pdb=" N   ASP A  20 "
           pdb=" CA  ASP A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.81  -22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" C3  PEV C 301 "
           pdb=" C1  PEV C 301 "
           pdb=" C2  PEV C 301 "
           pdb=" O3P PEV C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     292.80  164.82  127.98     1      3.00e+01 1.11e-03 1.72e+01
  dihedral pdb=" C3  PEV B 301 "
           pdb=" C1  PEV B 301 "
           pdb=" C2  PEV B 301 "
           pdb=" O3P PEV B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     292.80  172.73  120.07     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 5608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 968
       0.046 -    0.092: 424
       0.092 -    0.138: 60
       0.138 -    0.184: 10
       0.184 -    0.230: 3
  Chirality restraints: 1465
  Sorted by residual:
  chirality pdb=" C5  PGT A 301 "
            pdb=" C4  PGT A 301 "
            pdb=" C6  PGT A 301 "
            pdb=" O5  PGT A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.53    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" C2  PGT A 301 "
            pdb=" C1  PGT A 301 "
            pdb=" C3  PGT A 301 "
            pdb=" O2  PGT A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.55   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL B 197 "
            pdb=" CA  VAL B 197 "
            pdb=" CG1 VAL B 197 "
            pdb=" CG2 VAL B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 1462 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 113 "    0.017 2.00e-02 2.50e+03   1.73e-02 5.26e+00
        pdb=" CG  PHE A 113 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 113 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 113 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 113 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 113 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 113 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 140 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B 141 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 141 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 141 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 171 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO E 172 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO E 172 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 172 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 21
        2.42 -     3.04: 6027
        3.04 -     3.66: 13193
        3.66 -     4.28: 19345
        4.28 -     4.90: 32973
  Nonbonded interactions: 71559
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  98 "
            pdb=" NH1 ARG D 110 "
     model   vdw
     1.796 3.120
  nonbonded pdb=" OG  SER A  98 "
            pdb=" NH1 ARG A 110 "
     model   vdw
     2.179 3.120
  nonbonded pdb=" OE2 GLU A  58 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG1 THR A 148 "
            pdb=" O   ALA A 177 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE2 GLU B  58 "
            pdb=" OG  SER B  82 "
     model   vdw
     2.241 3.040
  ... (remaining 71554 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 11 through 233)
  selection = (chain 'B' and resid 11 through 233)
  selection = (chain 'C' and resid 11 through 233)
  selection = (chain 'D' and resid 11 through 233)
  selection = (chain 'E' and resid 11 through 233)
}
ncs_group {
  reference = (chain 'Y' and resid 12 through 40)
  selection = chain 'Z'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.460
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.030
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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      :  0.012   0.104   9317  Z= 0.732
  Angle     :  1.033  18.665  12570  Z= 0.504
  Chirality :  0.049   0.230   1465
  Planarity :  0.004   0.039   1598
  Dihedral  : 16.668 127.984   3433
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.78 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 10.99 %
    Favored  : 88.58 %
  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: -0.84 (0.22), residues: 1172
  helix:  0.18 (0.15), residues: 996
  sheet:  None (None), residues: 0
  loop : -4.46 (0.30), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E  38 
 HIS   0.009   0.001   HIS Z  16 
 PHE   0.040   0.003   PHE A 113 
 TYR   0.016   0.002   TYR D 132 
 ARG   0.009   0.001   ARG B 118 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8202 (tp30)
REVERT: B  126 MET cc_start: 0.8051 (mmm) cc_final: 0.7533 (mmt)
REVERT: C   64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: C   94 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5213 (mm-30)
REVERT: D  128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7521 (ttp-110)
REVERT: E  226 LEU cc_start: 0.8851 (mt) cc_final: 0.8548 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 152
  average time/residue: 0.2868
  time to fit residues: 56.3173
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain E residue  186 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
B  70 GLN
B  93 ASN
C 215 GLN
D  93 ASN
D 125 GLN
D 196 ASN
E  69 ASN
E  93 ASN
E 196 ASN
Z  16 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.169712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.134203 restraints weight = 10130.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.96
r_work: 0.3383 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9317  Z= 0.185
  Angle     :  0.519   6.805  12570  Z= 0.266
  Chirality :  0.035   0.127   1465
  Planarity :  0.003   0.030   1598
  Dihedral  : 12.078 126.590   1440
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.73 %
    Favored  : 82.44 %
  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:  1.94 (0.24), residues: 1172
  helix:  2.05 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -4.17 (0.35), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  38 
 HIS   0.003   0.000   HIS Z  16 
 PHE   0.019   0.001   PHE A 113 
 TYR   0.009   0.001   TYR A 132 
 ARG   0.006   0.000   ARG E 200 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.8904 (tp30) cc_final: 0.8699 (tp30)
REVERT: B   96 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7942 (mt-10)
REVERT: B  126 MET cc_start: 0.7660 (mmm) cc_final: 0.7398 (mmt)
REVERT: B  153 MET cc_start: 0.8550 (ttp) cc_final: 0.8225 (ttt)
REVERT: C   93 ASN cc_start: 0.8410 (t0) cc_final: 0.7931 (t0)
REVERT: C  118 ARG cc_start: 0.7232 (tpm170) cc_final: 0.6860 (mmm-85)
REVERT: D  200 ARG cc_start: 0.8093 (mmm160) cc_final: 0.6871 (mtp180)
REVERT: E  226 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: Z   15 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7863 (mtt)
  outliers start: 17
  outliers final: 7
  residues processed: 125
  average time/residue: 0.3016
  time to fit residues: 49.4759
Evaluate side-chains
  119 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain E residue   96 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Z residue   15 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 82 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.171539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.136118 restraints weight = 10310.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.96
r_work: 0.3400 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9317  Z= 0.173
  Angle     :  0.489   6.697  12570  Z= 0.248
  Chirality :  0.034   0.121   1465
  Planarity :  0.003   0.055   1598
  Dihedral  : 11.682 127.656   1439
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.03 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.00 (0.25), residues: 1172
  helix:  2.77 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.83 (0.37), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 
 PHE   0.014   0.001   PHE A 113 
 TYR   0.007   0.001   TYR D 132 
 ARG   0.004   0.000   ARG C 200 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8253 (pt0)
REVERT: B   94 GLU cc_start: 0.8908 (tp30) cc_final: 0.8590 (tp30)
REVERT: B   96 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: B  153 MET cc_start: 0.8557 (ttp) cc_final: 0.8173 (ttt)
REVERT: C  118 ARG cc_start: 0.7387 (tpm170) cc_final: 0.6950 (mmm-85)
REVERT: D  200 ARG cc_start: 0.8075 (mmm160) cc_final: 0.6909 (mtp180)
REVERT: E   99 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7838 (pt0)
REVERT: E  215 GLN cc_start: 0.8313 (tp40) cc_final: 0.7688 (tt0)
REVERT: E  226 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: Z   15 MET cc_start: 0.8147 (mtm) cc_final: 0.7863 (mtt)
  outliers start: 20
  outliers final: 10
  residues processed: 123
  average time/residue: 0.2647
  time to fit residues: 43.6039
Evaluate side-chains
  115 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 44 optimal weight:   30.0000
   chunk 84 optimal weight:    0.7980
   chunk 70 optimal weight:    0.1980
   chunk 76 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.188862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.154412 restraints weight = 9877.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.84
r_work: 0.3664 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9317  Z= 0.161
  Angle     :  0.472   6.725  12570  Z= 0.238
  Chirality :  0.034   0.181   1465
  Planarity :  0.003   0.042   1598
  Dihedral  : 11.235 123.475   1438
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.46 %
    Favored  : 79.85 %
  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:  3.50 (0.25), residues: 1172
  helix:  3.11 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.66 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 
 PHE   0.011   0.001   PHE A 113 
 TYR   0.014   0.001   TYR B  16 
 ARG   0.004   0.000   ARG E 200 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.613 
Fit side-chains
REVERT: A   64 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8098 (pt0)
REVERT: A  223 ASP cc_start: 0.7808 (m-30) cc_final: 0.7493 (m-30)
REVERT: B   96 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7787 (mt-10)
REVERT: B  126 MET cc_start: 0.7363 (mmp) cc_final: 0.6979 (mmt)
REVERT: B  153 MET cc_start: 0.8453 (ttp) cc_final: 0.8059 (ttt)
REVERT: D  200 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7004 (mtm-85)
REVERT: E  215 GLN cc_start: 0.8146 (tp40) cc_final: 0.7608 (tt0)
REVERT: E  226 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8277 (mp)
REVERT: Z   15 MET cc_start: 0.7782 (mtm) cc_final: 0.7577 (mtt)
  outliers start: 25
  outliers final: 15
  residues processed: 122
  average time/residue: 0.2842
  time to fit residues: 47.9778
Evaluate side-chains
  116 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 67 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.189079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.154195 restraints weight = 9976.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 1.87
r_work: 0.3662 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9317  Z= 0.164
  Angle     :  0.467   6.794  12570  Z= 0.236
  Chirality :  0.034   0.134   1465
  Planarity :  0.003   0.058   1598
  Dihedral  : 10.765 122.257   1438
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.10 %
    Favored  : 79.20 %
  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:  3.75 (0.25), residues: 1172
  helix:  3.26 (0.15), residues: 1015
  sheet:  None (None), residues: 0
  loop : -3.48 (0.40), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 
 PHE   0.010   0.001   PHE Z  23 
 TYR   0.006   0.001   TYR B 132 
 ARG   0.004   0.000   ARG E 200 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8076 (pt0)
REVERT: A  223 ASP cc_start: 0.7765 (m-30) cc_final: 0.7346 (m-30)
REVERT: B   96 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: B  126 MET cc_start: 0.7331 (mmp) cc_final: 0.7007 (mmt)
REVERT: B  153 MET cc_start: 0.8444 (ttp) cc_final: 0.8045 (ttt)
REVERT: D  128 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7258 (ttp-170)
REVERT: D  200 ARG cc_start: 0.7834 (mmm160) cc_final: 0.6932 (mtp180)
REVERT: E   99 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7586 (pt0)
REVERT: E  226 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (mp)
REVERT: Z   35 MET cc_start: 0.7793 (tpp) cc_final: 0.7525 (mmt)
  outliers start: 25
  outliers final: 17
  residues processed: 121
  average time/residue: 0.2603
  time to fit residues: 42.1543
Evaluate side-chains
  118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain E residue   96 GLU
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.187066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.152040 restraints weight = 9847.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.87
r_work: 0.3639 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9317  Z= 0.209
  Angle     :  0.491   6.810  12570  Z= 0.245
  Chirality :  0.035   0.119   1465
  Planarity :  0.003   0.047   1598
  Dihedral  : 10.604 118.499   1438
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.43 %
    Favored  : 78.88 %
  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:  3.73 (0.25), residues: 1172
  helix:  3.22 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.36 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.002   0.000   HIS Z  16 
 PHE   0.011   0.001   PHE A 113 
 TYR   0.007   0.001   TYR D 132 
 ARG   0.004   0.000   ARG A  66 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8077 (pt0)
REVERT: A  223 ASP cc_start: 0.7762 (m-30) cc_final: 0.7311 (m-30)
REVERT: B   96 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7836 (mt-10)
REVERT: B  126 MET cc_start: 0.7272 (mmp) cc_final: 0.6975 (mmt)
REVERT: B  153 MET cc_start: 0.8459 (ttp) cc_final: 0.8055 (ttt)
REVERT: C  114 ARG cc_start: 0.6387 (tpm170) cc_final: 0.6063 (tpm170)
REVERT: D  128 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7316 (ttp-170)
REVERT: D  153 MET cc_start: 0.6879 (ttp) cc_final: 0.6607 (ttt)
REVERT: D  200 ARG cc_start: 0.7617 (mmm160) cc_final: 0.6758 (mtm110)
REVERT: E   99 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7594 (pt0)
REVERT: E  208 MET cc_start: 0.8169 (ttp) cc_final: 0.7964 (ttm)
REVERT: E  226 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8212 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 126
  average time/residue: 0.2513
  time to fit residues: 42.3089
Evaluate side-chains
  125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 79 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
D 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.189594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.154759 restraints weight = 10022.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 1.87
r_work: 0.3660 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9317  Z= 0.156
  Angle     :  0.474   8.171  12570  Z= 0.238
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.041   1598
  Dihedral  : 10.316 114.900   1438
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.29 %
    Favored  : 78.02 %
  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:  3.94 (0.25), residues: 1172
  helix:  3.36 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.27 (0.42), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.003   0.000   HIS A  86 
 PHE   0.010   0.001   PHE Z  23 
 TYR   0.006   0.001   TYR B 132 
 ARG   0.006   0.000   ARG A 118 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8049 (pt0)
REVERT: A  181 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7506 (m)
REVERT: A  223 ASP cc_start: 0.7738 (m-30) cc_final: 0.7274 (m-30)
REVERT: B  126 MET cc_start: 0.7152 (mmp) cc_final: 0.6920 (mmt)
REVERT: B  153 MET cc_start: 0.8447 (ttp) cc_final: 0.8047 (ttt)
REVERT: C   64 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: C  118 ARG cc_start: 0.7134 (tpm170) cc_final: 0.6905 (mmm-85)
REVERT: D  128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7146 (ttp-170)
REVERT: D  153 MET cc_start: 0.6942 (ttp) cc_final: 0.6653 (ttt)
REVERT: D  200 ARG cc_start: 0.7326 (mmm160) cc_final: 0.6549 (mtm110)
REVERT: E   99 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7547 (pt0)
REVERT: E  226 LEU cc_start: 0.8507 (mt) cc_final: 0.8226 (mp)
REVERT: Z   15 MET cc_start: 0.6916 (mmt) cc_final: 0.6335 (mmt)
  outliers start: 25
  outliers final: 18
  residues processed: 130
  average time/residue: 0.2859
  time to fit residues: 48.9292
Evaluate side-chains
  123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 106 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
C 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.197639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160811 restraints weight = 10260.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.96
r_work: 0.3655 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9317  Z= 0.164
  Angle     :  0.479   8.054  12570  Z= 0.240
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.067   1598
  Dihedral  : 10.004 108.666   1437
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.40 %
    Favored  : 78.02 %
  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:  4.01 (0.25), residues: 1172
  helix:  3.40 (0.15), residues: 1018
  sheet:  None (None), residues: 0
  loop : -3.29 (0.43), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.002   0.000   HIS A  86 
 PHE   0.010   0.001   PHE Z  23 
 TYR   0.006   0.001   TYR C 132 
 ARG   0.009   0.000   ARG A 118 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8076 (pt0)
REVERT: A  181 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7605 (m)
REVERT: A  223 ASP cc_start: 0.7754 (m-30) cc_final: 0.7275 (m-30)
REVERT: B   94 GLU cc_start: 0.8853 (tp30) cc_final: 0.8650 (tp30)
REVERT: B  126 MET cc_start: 0.7160 (mmp) cc_final: 0.6949 (mmt)
REVERT: B  153 MET cc_start: 0.8436 (ttp) cc_final: 0.8032 (ttt)
REVERT: C   64 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: D  128 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7140 (ttp-170)
REVERT: D  153 MET cc_start: 0.6906 (ttp) cc_final: 0.6620 (ttt)
REVERT: D  200 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6685 (mtm110)
REVERT: E   99 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7588 (pt0)
REVERT: E  226 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (mp)
REVERT: Z   35 MET cc_start: 0.7673 (tpp) cc_final: 0.7462 (mmt)
  outliers start: 24
  outliers final: 18
  residues processed: 122
  average time/residue: 0.2768
  time to fit residues: 45.1532
Evaluate side-chains
  121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   77 ASP
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 88 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
E  93 ASN
Z  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.193407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.156450 restraints weight = 10112.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 1.94
r_work: 0.3600 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9317  Z= 0.266
  Angle     :  0.536   8.228  12570  Z= 0.267
  Chirality :  0.036   0.122   1465
  Planarity :  0.003   0.063   1598
  Dihedral  : 10.134 107.990   1437
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.50 %
    Favored  : 77.69 %
  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:  3.73 (0.25), residues: 1172
  helix:  3.22 (0.15), residues: 1014
  sheet:  None (None), residues: 0
  loop : -3.23 (0.43), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  38 
 HIS   0.002   0.000   HIS Z  16 
 PHE   0.011   0.001   PHE Z  23 
 TYR   0.008   0.001   TYR D 132 
 ARG   0.005   0.001   ARG A 118 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8100 (pt0)
REVERT: A  181 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7692 (m)
REVERT: A  223 ASP cc_start: 0.7790 (m-30) cc_final: 0.7333 (m-30)
REVERT: B  126 MET cc_start: 0.7247 (mmp) cc_final: 0.7022 (mmt)
REVERT: B  153 MET cc_start: 0.8460 (ttp) cc_final: 0.8050 (ttt)
REVERT: C   64 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8069 (tm-30)
REVERT: C  114 ARG cc_start: 0.6406 (tpm170) cc_final: 0.6077 (tpm170)
REVERT: D   15 MET cc_start: 0.7783 (tpp) cc_final: 0.7463 (tpp)
REVERT: D  200 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6641 (mtm110)
REVERT: E   99 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7615 (pt0)
REVERT: E  208 MET cc_start: 0.8190 (ttp) cc_final: 0.7980 (ttm)
REVERT: E  226 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: Z   35 MET cc_start: 0.7685 (tpp) cc_final: 0.7387 (mmt)
  outliers start: 26
  outliers final: 18
  residues processed: 133
  average time/residue: 0.2464
  time to fit residues: 43.8889
Evaluate side-chains
  132 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   93 ASN
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain E residue  226 LEU
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0040
   chunk 94 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 107 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
Z  16 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.189478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.154541 restraints weight = 10040.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.89
r_work: 0.3658 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9317  Z= 0.151
  Angle     :  0.477   8.658  12570  Z= 0.242
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.059   1598
  Dihedral  :  9.899 105.300   1437
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.15 %
    Favored  : 77.59 %
  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:  4.07 (0.25), residues: 1172
  helix:  3.44 (0.15), residues: 1016
  sheet:  None (None), residues: 0
  loop : -3.17 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 
 PHE   0.011   0.001   PHE Z  23 
 TYR   0.014   0.001   TYR C  16 
 ARG   0.005   0.000   ARG A 118 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8086 (pt0)
REVERT: A  181 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7673 (m)
REVERT: A  223 ASP cc_start: 0.7760 (m-30) cc_final: 0.7308 (m-30)
REVERT: B  153 MET cc_start: 0.8440 (ttp) cc_final: 0.8037 (ttt)
REVERT: C   64 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: D   15 MET cc_start: 0.7806 (tpp) cc_final: 0.7547 (tpp)
REVERT: D  153 MET cc_start: 0.6948 (ttp) cc_final: 0.6677 (ttt)
REVERT: D  200 ARG cc_start: 0.7348 (mmm160) cc_final: 0.6618 (mtm110)
REVERT: E   99 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7503 (pt0)
REVERT: E  226 LEU cc_start: 0.8501 (mt) cc_final: 0.8227 (mp)
REVERT: Z   35 MET cc_start: 0.7615 (tpp) cc_final: 0.7342 (mmt)
  outliers start: 21
  outliers final: 17
  residues processed: 122
  average time/residue: 0.2226
  time to fit residues: 37.4383
Evaluate side-chains
  121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   77 ASP
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   99 GLU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  186 VAL
Chi-restraints excluded: chain E residue  200 ARG
Chi-restraints excluded: chain Y residue   31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
C 201 GLN
Z  16 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.188775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.153696 restraints weight = 9966.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.89
r_work: 0.3658 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9317  Z= 0.169
  Angle     :  0.482   8.396  12570  Z= 0.243
  Chirality :  0.034   0.117   1465
  Planarity :  0.003   0.070   1598
  Dihedral  :  9.652  97.760   1437
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.69 %
    Favored  : 77.05 %
  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:  4.13 (0.25), residues: 1172
  helix:  3.47 (0.15), residues: 1018
  sheet:  None (None), residues: 0
  loop : -3.16 (0.45), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  38 
 HIS   0.001   0.000   HIS Z  16 
 PHE   0.010   0.001   PHE Z  23 
 TYR   0.012   0.001   TYR C  16 
 ARG   0.004   0.000   ARG E  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3764.13 seconds
wall clock time: 67 minutes 58.26 seconds (4078.26 seconds total)