Starting phenix.real_space_refine
on Tue Jun 10 21:53:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6q_28888/06_2025/8f6q_28888.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    7936      2.51       5
     N    2120      2.21       5
     O    2280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12352
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1544
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 3, 'TRANS': 195}
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 4.41, per 1000 atoms: 0.36
  Number of scatterers: 12352
  At special positions: 0
  Unit cell: (135.763, 135.763, 53.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    2280      8.00
     N    2120      7.00
     C    7936      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=0, symmetry=0
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3056

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      98.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 22
    Processing helix  chain 'A' and resid 24 through 48
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 149
    Processing helix  chain 'A' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 199
    Processing helix  chain 'B' and resid 2 through 22
    Processing helix  chain 'B' and resid 24 through 48
    Processing helix  chain 'B' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL B  54 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 149
    Processing helix  chain 'B' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 199
    Processing helix  chain 'C' and resid 2 through 22
    Processing helix  chain 'C' and resid 24 through 48
    Processing helix  chain 'C' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL C  54 " --> pdb=" O   ASP C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS C  79 " --> pdb=" O   GLU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 149
    Processing helix  chain 'C' and resid 151 through 172
      removed outlier: 3.782A  pdb=" N   GLU C 155 " --> pdb=" O   PRO C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 199
    Processing helix  chain 'D' and resid 2 through 22
    Processing helix  chain 'D' and resid 24 through 48
    Processing helix  chain 'D' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL D  54 " --> pdb=" O   ASP D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS D  79 " --> pdb=" O   GLU D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 149
    Processing helix  chain 'D' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU D 155 " --> pdb=" O   PRO D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 199
    Processing helix  chain 'E' and resid 2 through 22
    Processing helix  chain 'E' and resid 24 through 48
    Processing helix  chain 'E' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL E  54 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 99
      removed outlier: 4.140A  pdb=" N   LYS E  79 " --> pdb=" O   GLU E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL E 104 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 149
    Processing helix  chain 'E' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU E 155 " --> pdb=" O   PRO E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 199
    Processing helix  chain 'F' and resid 2 through 22
    Processing helix  chain 'F' and resid 24 through 48
    Processing helix  chain 'F' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL F  54 " --> pdb=" O   ASP F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS F  79 " --> pdb=" O   GLU F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL F 104 " --> pdb=" O   ASP F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 123 through 149
    Processing helix  chain 'F' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU F 155 " --> pdb=" O   PRO F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 173 through 199
    Processing helix  chain 'G' and resid 2 through 22
    Processing helix  chain 'G' and resid 24 through 48
    Processing helix  chain 'G' and resid 50 through 72
      removed outlier: 4.070A  pdb=" N   VAL G  54 " --> pdb=" O   ASP G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS G  79 " --> pdb=" O   GLU G  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL G 104 " --> pdb=" O   ASP G 100 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 123 through 149
    Processing helix  chain 'G' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU G 155 " --> pdb=" O   PRO G 151 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 173 through 199
    Processing helix  chain 'H' and resid 2 through 22
    Processing helix  chain 'H' and resid 24 through 48
    Processing helix  chain 'H' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL H  54 " --> pdb=" O   ASP H  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 99
      removed outlier: 4.140A  pdb=" N   LYS H  79 " --> pdb=" O   GLU H  75 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL H 104 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 123 through 149
    Processing helix  chain 'H' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU H 155 " --> pdb=" O   PRO H 151 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 173 through 199

    1273 hydrogen bonds defined for protein.
    3819 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: 3.94

  Time building geometry restraints manager: 3.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3054
        1.33 -     1.45: 2025
        1.45 -     1.57: 7417
        1.57 -     1.68: 0
        1.68 -     1.80: 32
  Bond restraints: 12528
  Sorted by residual:
  bond pdb=" N   ALA A  68 "
       pdb=" CA  ALA A  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.21e-02 6.83e+03 8.10e+00
  bond pdb=" N   ALA G  68 "
       pdb=" CA  ALA G  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.21e-02 6.83e+03 7.88e+00
  bond pdb=" N   ALA H  68 "
       pdb=" CA  ALA H  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.21e-02 6.83e+03 7.83e+00
  bond pdb=" N   ALA C  68 "
       pdb=" CA  ALA C  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.21e-02 6.83e+03 7.80e+00
  bond pdb=" N   ALA F  68 "
       pdb=" CA  ALA F  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.426  0.033 1.21e-02 6.83e+03 7.64e+00
  ... (remaining 12523 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 16800
        3.17 -     6.34: 80
        6.34 -     9.51: 0
        9.51 -    12.67: 0
       12.67 -    15.84: 8
  Bond angle restraints: 16888
  Sorted by residual:
  angle pdb=" CA  LEU C  67 "
        pdb=" CB  LEU C  67 "
        pdb=" CG  LEU C  67 "
      ideal   model   delta    sigma   weight residual
     116.30  100.46   15.84 3.50e+00 8.16e-02 2.05e+01
  angle pdb=" CA  LEU A  67 "
        pdb=" CB  LEU A  67 "
        pdb=" CG  LEU A  67 "
      ideal   model   delta    sigma   weight residual
     116.30  100.47   15.83 3.50e+00 8.16e-02 2.05e+01
  angle pdb=" CA  LEU H  67 "
        pdb=" CB  LEU H  67 "
        pdb=" CG  LEU H  67 "
      ideal   model   delta    sigma   weight residual
     116.30  100.47   15.83 3.50e+00 8.16e-02 2.05e+01
  angle pdb=" CA  LEU G  67 "
        pdb=" CB  LEU G  67 "
        pdb=" CG  LEU G  67 "
      ideal   model   delta    sigma   weight residual
     116.30  100.48   15.82 3.50e+00 8.16e-02 2.04e+01
  angle pdb=" CA  LEU B  67 "
        pdb=" CB  LEU B  67 "
        pdb=" CG  LEU B  67 "
      ideal   model   delta    sigma   weight residual
     116.30  100.48   15.82 3.50e+00 8.16e-02 2.04e+01
  ... (remaining 16883 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 7015
       17.82 -    35.63: 601
       35.63 -    53.45: 88
       53.45 -    71.26: 8
       71.26 -    89.08: 8
  Dihedral angle restraints: 7720
    sinusoidal: 3080
      harmonic: 4640
  Sorted by residual:
  dihedral pdb=" CB  GLU H  17 "
           pdb=" CG  GLU H  17 "
           pdb=" CD  GLU H  17 "
           pdb=" OE1 GLU H  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.08   89.08     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU D  17 "
           pdb=" CG  GLU D  17 "
           pdb=" CD  GLU D  17 "
           pdb=" OE1 GLU D  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.07   89.07     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU E  17 "
           pdb=" CG  GLU E  17 "
           pdb=" CD  GLU E  17 "
           pdb=" OE1 GLU E  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.05   89.05     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 7717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1596
       0.046 -    0.093: 284
       0.093 -    0.139: 40
       0.139 -    0.186: 0
       0.186 -    0.232: 16
  Chirality restraints: 1936
  Sorted by residual:
  chirality pdb=" CG  LEU B  67 "
            pdb=" CB  LEU B  67 "
            pdb=" CD1 LEU B  67 "
            pdb=" CD2 LEU B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CG  LEU C  67 "
            pdb=" CB  LEU C  67 "
            pdb=" CD1 LEU C  67 "
            pdb=" CD2 LEU C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CG  LEU H  67 "
            pdb=" CB  LEU H  67 "
            pdb=" CD1 LEU H  67 "
            pdb=" CD2 LEU H  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1933 not shown)

  Planarity restraints: 2152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  66 "   -0.008 2.00e-02 2.50e+03   1.62e-02 2.62e+00
        pdb=" C   GLU A  66 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLU A  66 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  67 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  66 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   GLU D  66 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLU D  66 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU D  67 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  66 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLU F  66 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLU F  66 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU F  67 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2149 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 408
        2.70 -     3.25: 13632
        3.25 -     3.80: 21466
        3.80 -     4.35: 23153
        4.35 -     4.90: 39479
  Nonbonded interactions: 98138
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 139 "
            pdb=" OE2 GLU D  66 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" NZ  LYS B 139 "
            pdb=" OE2 GLU C  66 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" OE1 GLU F  13 "
            pdb=" NH2 ARG F  16 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OE1 GLU H  13 "
            pdb=" NH2 ARG H  16 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OE1 GLU G  13 "
            pdb=" NH2 ARG G  16 "
     model   vdw
     2.208 3.120
  ... (remaining 98133 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'H'
}

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:             0.570
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     27.110
  Find NCS groups from input model:        0.260
  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:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
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   0.034  12528  Z= 0.336
  Angle     :  0.724  15.844  16888  Z= 0.418
  Chirality :  0.040   0.232   1936
  Planarity :  0.003   0.028   2152
  Dihedral  : 12.978  89.081   4664
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 20.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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:  0.52 (0.19), residues: 1576
  helix:  0.67 (0.12), residues: 1480
  sheet:  None (None), residues: 0
  loop : -3.60 (0.55), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E 113 
 PHE   0.006   0.001   PHE F 171 
 ARG   0.001   0.000   ARG E  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11830 ( 1273)
  hydrogen bonds       : angle       4.95624 ( 3819)
  covalent geometry    : bond        0.00613 (12528)
  covalent geometry    : angle       0.72436 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 362
  time to evaluate  : 1.391 
Fit side-chains
REVERT: A    7 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7280 (mmp-170)
REVERT: A   48 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A   50 ASP cc_start: 0.7753 (t0) cc_final: 0.7519 (t70)
REVERT: A  136 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A  146 MET cc_start: 0.8025 (tpt) cc_final: 0.7790 (tpt)
REVERT: A  173 ASP cc_start: 0.8326 (t0) cc_final: 0.8026 (t0)
REVERT: B    6 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7601 (mm-30)
REVERT: B    7 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7298 (mpt180)
REVERT: B   48 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: B  136 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: C    7 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7311 (mmp-170)
REVERT: C   48 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: C  136 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7948 (tm-30)
REVERT: C  146 MET cc_start: 0.7896 (tpt) cc_final: 0.7676 (tpt)
REVERT: C  173 ASP cc_start: 0.8238 (t0) cc_final: 0.7964 (t0)
REVERT: D    7 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7424 (mpt180)
REVERT: D   48 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7522 (mm-30)
REVERT: D  136 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: D  142 MET cc_start: 0.9079 (tpp) cc_final: 0.8551 (tpt)
REVERT: D  183 PHE cc_start: 0.8831 (t80) cc_final: 0.8565 (t80)
REVERT: E    6 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: E    7 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7246 (mmp-170)
REVERT: E   48 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7507 (mm-30)
REVERT: E  136 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: E  142 MET cc_start: 0.9067 (tpp) cc_final: 0.8657 (tpt)
REVERT: E  146 MET cc_start: 0.8033 (tpt) cc_final: 0.7749 (tpt)
REVERT: F    6 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: F    7 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7286 (mpt180)
REVERT: F   48 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7518 (mm-30)
REVERT: F  136 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: F  183 PHE cc_start: 0.8781 (t80) cc_final: 0.8580 (t80)
REVERT: G    6 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: G    7 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7036 (mmp-170)
REVERT: G   48 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: G  136 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: H    7 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7419 (mpt180)
REVERT: H   48 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7534 (mm-30)
REVERT: H  136 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: H  142 MET cc_start: 0.9041 (tpp) cc_final: 0.8629 (tpt)
REVERT: H  173 ASP cc_start: 0.8135 (t0) cc_final: 0.7933 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 362
  average time/residue: 0.3891
  time to fit residues: 177.9594
Evaluate side-chains
  161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0270
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 138 optimal weight:    4.9990
   overall best weight:    1.5842

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN
C  71 ASN
E  71 ASN
G  71 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.139074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.093737 restraints weight = 19280.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.096641 restraints weight = 11079.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098543 restraints weight = 7884.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12528  Z= 0.158
  Angle     :  0.542   8.658  16888  Z= 0.283
  Chirality :  0.032   0.153   1936
  Planarity :  0.003   0.029   2152
  Dihedral  :  3.429  13.184   1688
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.63 %
    Favored  : 88.51 %
  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:  2.74 (0.20), residues: 1576
  helix:  2.09 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -2.19 (0.60), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 152 
 PHE   0.015   0.001   PHE D 183 
 ARG   0.005   0.000   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04863 ( 1273)
  hydrogen bonds       : angle       3.71419 ( 3819)
  covalent geometry    : bond        0.00356 (12528)
  covalent geometry    : angle       0.54153 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 215
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.7536 (mtm180) cc_final: 0.7279 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: B    6 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: B    7 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7189 (mmp-170)
REVERT: B   24 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6893 (tm-30)
REVERT: B   47 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7263 (ttmm)
REVERT: B   48 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7284 (mm-30)
REVERT: B  136 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: C  136 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: C  142 MET cc_start: 0.9043 (tpp) cc_final: 0.8787 (tpt)
REVERT: D    4 ILE cc_start: 0.7880 (mm) cc_final: 0.7654 (tt)
REVERT: D    7 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7500 (mpt180)
REVERT: D   27 PHE cc_start: 0.7069 (t80) cc_final: 0.6868 (t80)
REVERT: D   73 ASP cc_start: 0.8237 (t70) cc_final: 0.8035 (t70)
REVERT: D  136 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: D  142 MET cc_start: 0.9036 (tpp) cc_final: 0.8466 (tpt)
REVERT: E    6 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: E    7 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7272 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: E  142 MET cc_start: 0.9144 (tpp) cc_final: 0.8800 (tpt)
REVERT: F    6 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: F    7 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7370 (mmp-170)
REVERT: F   47 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7328 (ttmt)
REVERT: F  136 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7820 (tm-30)
REVERT: F  169 GLU cc_start: 0.8455 (tp30) cc_final: 0.8199 (tt0)
REVERT: G    6 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: G    7 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7109 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: G  192 ILE cc_start: 0.8543 (tt) cc_final: 0.8230 (tt)
REVERT: H    4 ILE cc_start: 0.7873 (mm) cc_final: 0.7655 (tt)
REVERT: H    7 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7473 (mpt180)
REVERT: H   73 ASP cc_start: 0.7982 (t70) cc_final: 0.7774 (t70)
REVERT: H  136 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7831 (tm-30)
REVERT: H  142 MET cc_start: 0.9083 (tpp) cc_final: 0.8531 (tpt)
REVERT: H  169 GLU cc_start: 0.8378 (tp30) cc_final: 0.8092 (tt0)
REVERT: H  192 ILE cc_start: 0.8676 (tt) cc_final: 0.8389 (tt)
  outliers start: 22
  outliers final: 9
  residues processed: 230
  average time/residue: 0.2502
  time to fit residues: 82.3257
Evaluate side-chains
  169 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 160
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   chunk 110 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.138932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.094399 restraints weight = 19341.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.097264 restraints weight = 11140.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.099162 restraints weight = 7904.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12528  Z= 0.159
  Angle     :  0.519   6.802  16888  Z= 0.273
  Chirality :  0.031   0.112   1936
  Planarity :  0.003   0.027   2152
  Dihedral  :  3.341  13.600   1688
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 11.06 %
    Favored  : 85.81 %
  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:  3.54 (0.20), residues: 1576
  helix:  2.58 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.76 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 197 
 PHE   0.011   0.001   PHE G 183 
 ARG   0.003   0.000   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 ( 1273)
  hydrogen bonds       : angle       3.59828 ( 3819)
  covalent geometry    : bond        0.00363 (12528)
  covalent geometry    : angle       0.51869 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 1.548 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7313 (pttt)
REVERT: A  136 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: B    7 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7267 (mmp-170)
REVERT: B   47 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7366 (ttmt)
REVERT: B   73 ASP cc_start: 0.8074 (t70) cc_final: 0.7839 (t70)
REVERT: B  132 GLU cc_start: 0.7839 (tp30) cc_final: 0.7622 (tp30)
REVERT: B  136 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: C  136 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: C  142 MET cc_start: 0.9062 (tpp) cc_final: 0.8705 (tpt)
REVERT: D    7 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7534 (mpt180)
REVERT: D   47 LYS cc_start: 0.7853 (mmtm) cc_final: 0.6958 (ttmt)
REVERT: D   73 ASP cc_start: 0.8189 (t70) cc_final: 0.7870 (t70)
REVERT: D  123 ASP cc_start: 0.8281 (t0) cc_final: 0.8020 (t0)
REVERT: D  136 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: D  146 MET cc_start: 0.8280 (tmm) cc_final: 0.7908 (tmm)
REVERT: E    6 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: E    7 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7327 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7120 (ttmt)
REVERT: E  136 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: F    7 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7414 (mmp-170)
REVERT: F  136 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: F  169 GLU cc_start: 0.8465 (tp30) cc_final: 0.8188 (tt0)
REVERT: G    6 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: G    7 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7200 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7148 (ttmm)
REVERT: G   73 ASP cc_start: 0.8050 (t70) cc_final: 0.7849 (t70)
REVERT: G  136 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: G  155 GLU cc_start: 0.7798 (tt0) cc_final: 0.7575 (tt0)
REVERT: H    7 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7495 (mpt180)
REVERT: H   24 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6848 (tm-30)
REVERT: H   47 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7007 (ttmt)
REVERT: H   73 ASP cc_start: 0.7954 (t70) cc_final: 0.7657 (t70)
REVERT: H  136 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: H  142 MET cc_start: 0.9128 (tpp) cc_final: 0.8476 (tpt)
REVERT: H  155 GLU cc_start: 0.7947 (tt0) cc_final: 0.7667 (tt0)
REVERT: H  169 GLU cc_start: 0.8430 (tp30) cc_final: 0.8194 (tt0)
REVERT: H  192 ILE cc_start: 0.8558 (tt) cc_final: 0.8334 (tt)
  outliers start: 37
  outliers final: 9
  residues processed: 239
  average time/residue: 0.2410
  time to fit residues: 83.3914
Evaluate side-chains
  170 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 133 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0470
   chunk 151 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.9680

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.140935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.095633 restraints weight = 19430.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.098597 restraints weight = 11287.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.100622 restraints weight = 8073.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12528  Z= 0.130
  Angle     :  0.475   8.683  16888  Z= 0.252
  Chirality :  0.030   0.107   1936
  Planarity :  0.003   0.024   2152
  Dihedral  :  3.298  13.189   1688
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.68 %
    Favored  : 84.46 %
  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:  3.98 (0.20), residues: 1576
  helix:  2.87 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.56 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 197 
 PHE   0.017   0.001   PHE D  27 
 ARG   0.003   0.000   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04320 ( 1273)
  hydrogen bonds       : angle       3.48547 ( 3819)
  covalent geometry    : bond        0.00284 (12528)
  covalent geometry    : angle       0.47486 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 1.437 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7294 (pttt)
REVERT: A  136 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: B    7 ARG cc_start: 0.7672 (mtm180) cc_final: 0.7279 (mpt180)
REVERT: B   47 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7358 (ttmt)
REVERT: B   73 ASP cc_start: 0.7995 (t70) cc_final: 0.7764 (t70)
REVERT: B  136 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: C   32 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: C   47 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6994 (pttt)
REVERT: C  136 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: D    7 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7586 (mpt180)
REVERT: D   47 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7043 (ttmt)
REVERT: D   67 LEU cc_start: 0.9035 (mm) cc_final: 0.8691 (mm)
REVERT: D   73 ASP cc_start: 0.8179 (t70) cc_final: 0.7809 (t70)
REVERT: D  136 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: D  146 MET cc_start: 0.8239 (tmm) cc_final: 0.7949 (tmm)
REVERT: E    6 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: E    7 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7410 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7377 (pttt)
REVERT: E  136 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: F    7 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7398 (mpt180)
REVERT: F   47 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7094 (ttmt)
REVERT: F  136 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: G    6 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: G    7 ARG cc_start: 0.7584 (mtm180) cc_final: 0.7228 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7444 (pttt)
REVERT: G   73 ASP cc_start: 0.7951 (t70) cc_final: 0.7696 (t70)
REVERT: G  136 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: H    7 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7592 (mpt180)
REVERT: H   47 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7134 (pttt)
REVERT: H   73 ASP cc_start: 0.7919 (t70) cc_final: 0.7551 (t70)
REVERT: H   82 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: H  136 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: H  155 GLU cc_start: 0.7919 (tt0) cc_final: 0.7672 (tt0)
  outliers start: 22
  outliers final: 10
  residues processed: 235
  average time/residue: 0.2439
  time to fit residues: 82.2165
Evaluate side-chains
  172 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 151 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 140 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 110 optimal weight:    0.7980
   chunk 121 optimal weight:    9.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.141859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.097732 restraints weight = 19236.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.100663 restraints weight = 11278.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.102613 restraints weight = 8056.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12528  Z= 0.126
  Angle     :  0.482   8.855  16888  Z= 0.253
  Chirality :  0.031   0.111   1936
  Planarity :  0.002   0.022   2152
  Dihedral  :  3.269  12.975   1688
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.79 %
    Favored  : 81.59 %
  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:  4.19 (0.20), residues: 1576
  helix:  3.03 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.55 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP G 197 
 PHE   0.021   0.001   PHE F  27 
 ARG   0.004   0.000   ARG G  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04218 ( 1273)
  hydrogen bonds       : angle       3.43498 ( 3819)
  covalent geometry    : bond        0.00277 (12528)
  covalent geometry    : angle       0.48154 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 1.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7320 (pttt)
REVERT: A  136 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: B    7 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7389 (mpt180)
REVERT: B   47 LYS cc_start: 0.7867 (mmtm) cc_final: 0.7228 (ttmm)
REVERT: B   73 ASP cc_start: 0.7955 (t70) cc_final: 0.7708 (t70)
REVERT: B  136 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: C   47 LYS cc_start: 0.7650 (mmtm) cc_final: 0.7036 (pttt)
REVERT: C  136 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7817 (tm-30)
REVERT: D    7 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7644 (mpt180)
REVERT: D   47 LYS cc_start: 0.7695 (mmtm) cc_final: 0.7071 (pttt)
REVERT: D   67 LEU cc_start: 0.9063 (mm) cc_final: 0.8562 (mm)
REVERT: D   73 ASP cc_start: 0.8144 (t70) cc_final: 0.7747 (t70)
REVERT: D  136 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: D  143 GLU cc_start: 0.8504 (tp30) cc_final: 0.8108 (tm-30)
REVERT: E    7 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7422 (mmp-170)
REVERT: E   73 ASP cc_start: 0.7785 (t70) cc_final: 0.7575 (t70)
REVERT: E  136 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: F    7 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7474 (mpt180)
REVERT: F   47 LYS cc_start: 0.7741 (mmtm) cc_final: 0.6998 (ttmt)
REVERT: F  136 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7816 (tm-30)
REVERT: G    6 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: G    7 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7233 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7462 (pttt)
REVERT: G   73 ASP cc_start: 0.7814 (t70) cc_final: 0.7592 (t70)
REVERT: G  136 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: H    7 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7601 (mpt180)
REVERT: H   47 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7154 (pttt)
REVERT: H   67 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8819 (mm)
REVERT: H   73 ASP cc_start: 0.7830 (t70) cc_final: 0.7469 (t70)
REVERT: H   82 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: H  136 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: H  155 GLU cc_start: 0.7947 (tt0) cc_final: 0.7695 (tt0)
  outliers start: 31
  outliers final: 13
  residues processed: 230
  average time/residue: 0.2498
  time to fit residues: 84.1306
Evaluate side-chains
  186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9980
   chunk 125 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
D  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.095312 restraints weight = 19531.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.098148 restraints weight = 11381.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.100147 restraints weight = 8150.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12528  Z= 0.145
  Angle     :  0.506   9.131  16888  Z= 0.265
  Chirality :  0.032   0.127   1936
  Planarity :  0.003   0.017   2152
  Dihedral  :  3.254  12.813   1688
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.31 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.15 (0.19), residues: 1576
  helix:  3.03 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.70 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP G 197 
 PHE   0.021   0.001   PHE H  27 
 ARG   0.004   0.000   ARG G  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 ( 1273)
  hydrogen bonds       : angle       3.45873 ( 3819)
  covalent geometry    : bond        0.00331 (12528)
  covalent geometry    : angle       0.50599 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7318 (pttt)
REVERT: A  121 ASN cc_start: 0.8380 (t0) cc_final: 0.8130 (t0)
REVERT: A  136 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: B    7 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7361 (mpt180)
REVERT: B   67 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8822 (mm)
REVERT: B   73 ASP cc_start: 0.7960 (t70) cc_final: 0.7685 (t70)
REVERT: B  136 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7805 (tm-30)
REVERT: C   47 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7059 (pttt)
REVERT: C  136 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: D    7 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7631 (mpt180)
REVERT: D   47 LYS cc_start: 0.7733 (mmtm) cc_final: 0.6926 (ttmt)
REVERT: D   67 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8694 (mm)
REVERT: D   73 ASP cc_start: 0.8025 (t70) cc_final: 0.7726 (t70)
REVERT: D  136 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: D  143 GLU cc_start: 0.8513 (tp30) cc_final: 0.8122 (tm-30)
REVERT: E    7 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7473 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7419 (pttt)
REVERT: E  121 ASN cc_start: 0.8466 (t0) cc_final: 0.8221 (t0)
REVERT: E  136 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: F    7 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7451 (mpt180)
REVERT: F   47 LYS cc_start: 0.7778 (mmtm) cc_final: 0.6966 (ttmt)
REVERT: F  136 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: G    6 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8050 (mm-30)
REVERT: G    7 ARG cc_start: 0.7607 (mtm180) cc_final: 0.7264 (mmp-170)
REVERT: G   71 ASN cc_start: 0.7065 (m-40) cc_final: 0.6811 (m-40)
REVERT: G   73 ASP cc_start: 0.7761 (t70) cc_final: 0.7495 (t70)
REVERT: G  121 ASN cc_start: 0.8421 (t0) cc_final: 0.8169 (t0)
REVERT: G  136 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: H    7 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7544 (mpt180)
REVERT: H   47 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7143 (pttt)
REVERT: H   67 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8842 (mm)
REVERT: H   73 ASP cc_start: 0.7841 (t70) cc_final: 0.7477 (t70)
REVERT: H   82 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: H  136 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: H  155 GLU cc_start: 0.7971 (tt0) cc_final: 0.7734 (tt0)
  outliers start: 35
  outliers final: 14
  residues processed: 213
  average time/residue: 0.2507
  time to fit residues: 77.3347
Evaluate side-chains
  177 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 1.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain G residue  197 TRP
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 138 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.137588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.093622 restraints weight = 19330.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.096368 restraints weight = 11305.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.098241 restraints weight = 8114.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12528  Z= 0.163
  Angle     :  0.528   8.462  16888  Z= 0.279
  Chirality :  0.034   0.238   1936
  Planarity :  0.003   0.021   2152
  Dihedral  :  3.316  12.931   1688
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.40 %
    Favored  : 79.90 %
  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:  4.04 (0.19), residues: 1576
  helix:  2.96 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.65 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 197 
 PHE   0.023   0.002   PHE H  27 
 ARG   0.004   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04688 ( 1273)
  hydrogen bonds       : angle       3.51648 ( 3819)
  covalent geometry    : bond        0.00377 (12528)
  covalent geometry    : angle       0.52794 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7317 (pttt)
REVERT: A  121 ASN cc_start: 0.8493 (t0) cc_final: 0.8232 (t0)
REVERT: A  136 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: B    7 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7446 (mpt180)
REVERT: B   47 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7004 (ttmt)
REVERT: B   67 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8820 (mm)
REVERT: B   73 ASP cc_start: 0.7962 (t70) cc_final: 0.7707 (t70)
REVERT: B  136 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: C  136 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: D    7 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7529 (mpt180)
REVERT: D   67 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8797 (mm)
REVERT: D   73 ASP cc_start: 0.8026 (t70) cc_final: 0.7624 (t70)
REVERT: D  136 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: D  143 GLU cc_start: 0.8484 (tp30) cc_final: 0.8168 (tm-30)
REVERT: E    7 ARG cc_start: 0.7734 (mtm180) cc_final: 0.7452 (mmp-170)
REVERT: E  121 ASN cc_start: 0.8577 (t0) cc_final: 0.8351 (t0)
REVERT: E  136 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7932 (tm-30)
REVERT: F    7 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7461 (mpt180)
REVERT: F   47 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7022 (ttmt)
REVERT: F   67 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8814 (mm)
REVERT: F  136 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: G    6 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8049 (mm-30)
REVERT: G    7 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7315 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7368 (pttt)
REVERT: G   73 ASP cc_start: 0.7741 (t70) cc_final: 0.7497 (t70)
REVERT: G  121 ASN cc_start: 0.8535 (t0) cc_final: 0.8287 (t0)
REVERT: G  136 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: H    7 ARG cc_start: 0.7817 (mtm180) cc_final: 0.7526 (mpt180)
REVERT: H   67 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8852 (mm)
REVERT: H   73 ASP cc_start: 0.7903 (t70) cc_final: 0.7518 (t70)
REVERT: H  136 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: H  155 GLU cc_start: 0.8008 (tt0) cc_final: 0.7798 (tt0)
  outliers start: 32
  outliers final: 17
  residues processed: 203
  average time/residue: 0.2257
  time to fit residues: 66.8224
Evaluate side-chains
  175 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain G residue  197 TRP
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 141 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 108 optimal weight:    2.9990
   chunk 151 optimal weight:    0.5980
   chunk 6 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
F  71 ASN
H  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.141095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.096882 restraints weight = 19397.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.099791 restraints weight = 11219.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.101727 restraints weight = 7998.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12528  Z= 0.134
  Angle     :  0.510   8.852  16888  Z= 0.268
  Chirality :  0.034   0.317   1936
  Planarity :  0.002   0.019   2152
  Dihedral  :  3.339  12.545   1688
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.75 %
    Favored  : 79.48 %
  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 (0.19), residues: 1576
  helix:  2.98 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.63 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 197 
 PHE   0.023   0.001   PHE H  27 
 ARG   0.004   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 ( 1273)
  hydrogen bonds       : angle       3.51589 ( 3819)
  covalent geometry    : bond        0.00297 (12528)
  covalent geometry    : angle       0.50996 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 183
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8373 (t0) cc_final: 0.8102 (t0)
REVERT: A  136 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: B    7 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7452 (mpt180)
REVERT: B   47 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7094 (ttmt)
REVERT: B   73 ASP cc_start: 0.8019 (t70) cc_final: 0.7745 (t70)
REVERT: B  136 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: C  136 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: D    7 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7558 (mpt180)
REVERT: D   47 LYS cc_start: 0.7666 (mmtm) cc_final: 0.6831 (ttmm)
REVERT: D   73 ASP cc_start: 0.7909 (t70) cc_final: 0.7587 (t70)
REVERT: D  136 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: D  143 GLU cc_start: 0.8517 (tp30) cc_final: 0.8107 (tm-30)
REVERT: E    7 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7464 (mmp-170)
REVERT: E  121 ASN cc_start: 0.8433 (t0) cc_final: 0.8175 (t0)
REVERT: E  136 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: F    7 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7427 (mpt180)
REVERT: F   47 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7084 (ttmt)
REVERT: F   67 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8808 (mm)
REVERT: F  136 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: G    7 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7263 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7386 (pttt)
REVERT: G   73 ASP cc_start: 0.7635 (t70) cc_final: 0.7411 (t70)
REVERT: G  121 ASN cc_start: 0.8422 (t0) cc_final: 0.8161 (t0)
REVERT: G  136 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: H    7 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7482 (mpt180)
REVERT: H   47 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6839 (ttmt)
REVERT: H   67 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8820 (mm)
REVERT: H   73 ASP cc_start: 0.7888 (t70) cc_final: 0.7533 (t70)
REVERT: H  136 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: H  155 GLU cc_start: 0.7903 (tt0) cc_final: 0.7677 (tt0)
  outliers start: 21
  outliers final: 15
  residues processed: 201
  average time/residue: 0.2338
  time to fit residues: 68.5544
Evaluate side-chains
  179 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 141 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
F  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.140633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095756 restraints weight = 19355.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.098664 restraints weight = 11269.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.100618 restraints weight = 8069.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12528  Z= 0.130
  Angle     :  0.535  14.607  16888  Z= 0.274
  Chirality :  0.034   0.326   1936
  Planarity :  0.002   0.017   2152
  Dihedral  :  3.296  13.089   1688
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.26 %
    Favored  : 78.63 %
  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:  4.16 (0.19), residues: 1576
  helix:  3.03 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.55 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 197 
 PHE   0.023   0.001   PHE B  27 
 ARG   0.004   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 ( 1273)
  hydrogen bonds       : angle       3.49541 ( 3819)
  covalent geometry    : bond        0.00287 (12528)
  covalent geometry    : angle       0.53521 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8380 (t0) cc_final: 0.8094 (t0)
REVERT: A  136 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: B    7 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7379 (mpt180)
REVERT: B   47 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7027 (ttmt)
REVERT: B   67 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8783 (mm)
REVERT: B   73 ASP cc_start: 0.7997 (t70) cc_final: 0.7765 (t70)
REVERT: B  136 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: C  136 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: C  143 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: D    7 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7530 (mpt180)
REVERT: D   47 LYS cc_start: 0.7659 (mmtm) cc_final: 0.6855 (ttmm)
REVERT: D   67 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8859 (mm)
REVERT: D   73 ASP cc_start: 0.7882 (t70) cc_final: 0.7564 (t70)
REVERT: D  136 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7864 (tm-30)
REVERT: D  143 GLU cc_start: 0.8520 (tp30) cc_final: 0.8078 (tm-30)
REVERT: E    7 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7467 (mmp-170)
REVERT: E  121 ASN cc_start: 0.8414 (t0) cc_final: 0.8148 (t0)
REVERT: E  136 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: F    7 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7491 (mpt180)
REVERT: F   47 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7099 (ttmt)
REVERT: F   67 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8824 (mm)
REVERT: F  136 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: G    7 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7332 (mmp-170)
REVERT: G   10 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6429 (tp30)
REVERT: G   73 ASP cc_start: 0.7658 (t70) cc_final: 0.7393 (t70)
REVERT: G  121 ASN cc_start: 0.8369 (t0) cc_final: 0.8092 (t0)
REVERT: G  136 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: H    7 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7596 (mmp-170)
REVERT: H   47 LYS cc_start: 0.7600 (mmtm) cc_final: 0.6863 (ttmt)
REVERT: H   67 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8819 (mm)
REVERT: H   73 ASP cc_start: 0.7851 (t70) cc_final: 0.7455 (t70)
REVERT: H  136 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7784 (tm-30)
REVERT: H  155 GLU cc_start: 0.7945 (tt0) cc_final: 0.7727 (tt0)
  outliers start: 25
  outliers final: 17
  residues processed: 198
  average time/residue: 0.2429
  time to fit residues: 70.7736
Evaluate side-chains
  186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 137 optimal weight:    0.0370
   chunk 60 optimal weight:    6.9990
   chunk 115 optimal weight:    5.9990
   chunk 151 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.9060

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.142229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.097646 restraints weight = 19232.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100515 restraints weight = 11284.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102434 restraints weight = 8107.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12528  Z= 0.130
  Angle     :  0.555  16.883  16888  Z= 0.282
  Chirality :  0.034   0.306   1936
  Planarity :  0.002   0.016   2152
  Dihedral  :  3.306  12.553   1688
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.85 %
    Favored  : 78.38 %
  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:  4.14 (0.19), residues: 1576
  helix:  3.02 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.57 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 197 
 PHE   0.022   0.001   PHE H  27 
 ARG   0.004   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 ( 1273)
  hydrogen bonds       : angle       3.50905 ( 3819)
  covalent geometry    : bond        0.00289 (12528)
  covalent geometry    : angle       0.55470 (16888)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7276 (pttt)
REVERT: A  136 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: B    7 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7399 (mpt180)
REVERT: B   47 LYS cc_start: 0.7747 (mmtm) cc_final: 0.6988 (ttmt)
REVERT: B   67 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8797 (mm)
REVERT: B   73 ASP cc_start: 0.7943 (t70) cc_final: 0.7660 (t70)
REVERT: B  136 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: C  136 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: C  143 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: D    7 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7533 (mpt180)
REVERT: D   47 LYS cc_start: 0.7488 (mmtm) cc_final: 0.7033 (pttt)
REVERT: D   67 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8853 (mm)
REVERT: D   73 ASP cc_start: 0.7891 (t70) cc_final: 0.7509 (t70)
REVERT: D  136 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: D  143 GLU cc_start: 0.8514 (tp30) cc_final: 0.8074 (tm-30)
REVERT: E    7 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7536 (mmp-170)
REVERT: E  121 ASN cc_start: 0.8395 (t0) cc_final: 0.8120 (t0)
REVERT: E  136 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7977 (tm-30)
REVERT: F    7 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7414 (mmp-170)
REVERT: F   47 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7094 (ttmt)
REVERT: F   67 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8788 (mm)
REVERT: F  136 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: G    7 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7328 (mmp-170)
REVERT: G   73 ASP cc_start: 0.7676 (t70) cc_final: 0.7405 (t70)
REVERT: G  136 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: H    7 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7567 (mmp-170)
REVERT: H   47 LYS cc_start: 0.7471 (mmtm) cc_final: 0.7020 (pttt)
REVERT: H   67 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: H   73 ASP cc_start: 0.7884 (t70) cc_final: 0.7490 (t70)
REVERT: H  136 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: H  155 GLU cc_start: 0.7952 (tt0) cc_final: 0.7735 (tt0)
  outliers start: 21
  outliers final: 16
  residues processed: 193
  average time/residue: 0.2292
  time to fit residues: 65.0479
Evaluate side-chains
  181 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 118 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.141154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096167 restraints weight = 19452.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.099103 restraints weight = 11300.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.101050 restraints weight = 8067.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12528  Z= 0.131
  Angle     :  0.557  15.397  16888  Z= 0.282
  Chirality :  0.034   0.329   1936
  Planarity :  0.002   0.017   2152
  Dihedral  :  3.304  12.560   1688
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.68 %
    Favored  : 78.55 %
  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:  4.13 (0.19), residues: 1576
  helix:  3.01 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.56 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP G 197 
 PHE   0.022   0.001   PHE H  27 
 ARG   0.004   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 ( 1273)
  hydrogen bonds       : angle       3.51700 ( 3819)
  covalent geometry    : bond        0.00293 (12528)
  covalent geometry    : angle       0.55693 (16888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3711.41 seconds
wall clock time: 65 minutes 5.19 seconds (3905.19 seconds total)