Starting phenix.real_space_refine
on Sat Aug 23 12:37:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6q_28888/08_2025/8f6q_28888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6q_28888/08_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_28888/08_2025/8f6q_28888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6q_28888/08_2025/8f6q_28888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6q_28888/08_2025/8f6q_28888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6q_28888/08_2025/8f6q_28888.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E, F, G, H
  Time building chain proxies: 1.32, per 1000 atoms: 0.11
  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: 0.99
  Conformation dependent library (CDL) restraints added in 495.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.35
  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: 2.02

  Time building geometry restraints manager: 1.27 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  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:             0.620
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     9.520
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.660
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (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
 ARG   0.001   0.000   ARG E  21 
 PHE   0.006   0.001   PHE F 171 
 TRP   0.008   0.002   TRP E 113 

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

*********************** 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  : 0.525 
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: 0.1645
  time to fit residues: 75.7095
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  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.139270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093967 restraints weight = 19414.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.096897 restraints weight = 11095.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.098814 restraints weight = 7876.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100034 restraints weight = 6426.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.100683 restraints weight = 5708.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2478

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= 0.157
  Angle     :  0.541   8.659  16888  Z= 0.283
  Chirality :  0.032   0.147   1936
  Planarity :  0.003   0.030   2152
  Dihedral  :  3.430  13.119   1688
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.63 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.74 (0.20), residues: 1576
  helix:  2.08 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -2.18 (0.60), residues: 104

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12528)
  covalent geometry    : angle       0.54105 (16888)
  hydrogen bonds       : bond        0.04845 ( 1273)
  hydrogen bonds       : angle       3.71111 ( 3819)

*********************** 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
  235 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 214
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7269 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: B    6 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7428 (mm-30)
REVERT: B    7 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7195 (mmp-170)
REVERT: B   24 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6877 (tm-30)
REVERT: B   47 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7379 (ttmt)
REVERT: B  136 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: C  136 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: C  142 MET cc_start: 0.9030 (tpp) cc_final: 0.8739 (tpt)
REVERT: D    4 ILE cc_start: 0.7890 (mm) cc_final: 0.7672 (tt)
REVERT: D    7 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7509 (mpt180)
REVERT: D   27 PHE cc_start: 0.7083 (t80) cc_final: 0.6877 (t80)
REVERT: D  136 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: D  142 MET cc_start: 0.9023 (tpp) cc_final: 0.8453 (tpt)
REVERT: D  169 GLU cc_start: 0.8552 (tp30) cc_final: 0.8277 (tt0)
REVERT: E    6 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8068 (mm-30)
REVERT: E    7 ARG cc_start: 0.7541 (mtm180) cc_final: 0.7238 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: E  142 MET cc_start: 0.9131 (tpp) cc_final: 0.8784 (tpt)
REVERT: F    6 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: F    7 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7370 (mmp-170)
REVERT: F   47 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7329 (ttmt)
REVERT: F  136 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: F  169 GLU cc_start: 0.8438 (tp30) cc_final: 0.8174 (tt0)
REVERT: G    6 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: G    7 ARG cc_start: 0.7468 (mtm180) cc_final: 0.7107 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: G  192 ILE cc_start: 0.8507 (tt) cc_final: 0.8192 (tt)
REVERT: H    4 ILE cc_start: 0.7880 (mm) cc_final: 0.7670 (tt)
REVERT: H    7 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7477 (mpt180)
REVERT: H  136 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: H  142 MET cc_start: 0.9071 (tpp) cc_final: 0.8528 (tpt)
REVERT: H  169 GLU cc_start: 0.8371 (tp30) cc_final: 0.8085 (tt0)
REVERT: H  192 ILE cc_start: 0.8649 (tt) cc_final: 0.8362 (tt)
  outliers start: 21
  outliers final: 9
  residues processed: 228
  average time/residue: 0.1047
  time to fit residues: 34.2029
Evaluate side-chains
  172 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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 88 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 134 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.134921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.089458 restraints weight = 19640.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.092159 restraints weight = 11472.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.093917 restraints weight = 8268.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.095027 restraints weight = 6808.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.095767 restraints weight = 6069.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12528  Z= 0.236
  Angle     :  0.613   6.410  16888  Z= 0.320
  Chirality :  0.034   0.130   1936
  Planarity :  0.004   0.032   2152
  Dihedral  :  3.475  13.116   1688
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 11.82 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.18 (0.20), residues: 1576
  helix:  2.38 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -2.05 (0.64), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 177 
 PHE   0.013   0.002   PHE G 183 
 TRP   0.010   0.002   TRP E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (12528)
  covalent geometry    : angle       0.61319 (16888)
  hydrogen bonds       : bond        0.05529 ( 1273)
  hydrogen bonds       : angle       3.79815 ( 3819)

*********************** 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
  222 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 176
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A    7 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7373 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7953 (tm-30)
REVERT: B    7 ARG cc_start: 0.7683 (mtm180) cc_final: 0.7288 (mpt180)
REVERT: B   73 ASP cc_start: 0.8101 (t70) cc_final: 0.7894 (t70)
REVERT: B  136 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: C  136 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: C  142 MET cc_start: 0.9055 (tpp) cc_final: 0.8420 (tpt)
REVERT: C  143 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: D    7 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7538 (mpt180)
REVERT: D   50 ASP cc_start: 0.8044 (t0) cc_final: 0.7643 (t70)
REVERT: D   73 ASP cc_start: 0.8311 (t70) cc_final: 0.8072 (t70)
REVERT: D  123 ASP cc_start: 0.8313 (t0) cc_final: 0.8096 (t0)
REVERT: D  136 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: D  142 MET cc_start: 0.8898 (tpp) cc_final: 0.8399 (tpt)
REVERT: D  143 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: D  169 GLU cc_start: 0.8586 (tp30) cc_final: 0.8355 (tt0)
REVERT: E    6 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8070 (mm-30)
REVERT: E    7 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7302 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: F    7 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7476 (mpt180)
REVERT: F  136 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: F  143 GLU cc_start: 0.8475 (tp30) cc_final: 0.8193 (tm-30)
REVERT: F  169 GLU cc_start: 0.8504 (tp30) cc_final: 0.8197 (tt0)
REVERT: G    6 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8076 (mm-30)
REVERT: G    7 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7195 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7130 (ttmt)
REVERT: G  136 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: H    7 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7495 (mpt180)
REVERT: H  136 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: H  143 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: H  169 GLU cc_start: 0.8475 (tp30) cc_final: 0.8202 (tt0)
  outliers start: 46
  outliers final: 16
  residues processed: 211
  average time/residue: 0.0983
  time to fit residues: 30.2644
Evaluate side-chains
  166 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 SER
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  133 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  133 SER
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  133 SER
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  133 SER
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue  133 SER
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain G residue  197 TRP
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 86 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 151 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 147 optimal weight:    0.9980
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.095310 restraints weight = 19596.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.098278 restraints weight = 11283.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.100243 restraints weight = 8015.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.101510 restraints weight = 6521.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.102179 restraints weight = 5778.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12528  Z= 0.130
  Angle     :  0.468   7.935  16888  Z= 0.250
  Chirality :  0.030   0.104   1936
  Planarity :  0.003   0.028   2152
  Dihedral  :  3.387  12.441   1688
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.78 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.76 (0.20), residues: 1576
  helix:  2.72 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.49 (0.65), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 177 
 PHE   0.011   0.001   PHE C  27 
 TRP   0.012   0.001   TRP E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12528)
  covalent geometry    : angle       0.46760 (16888)
  hydrogen bonds       : bond        0.04355 ( 1273)
  hydrogen bonds       : angle       3.55042 ( 3819)

*********************** 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
  243 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7360 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: B    7 ARG cc_start: 0.7716 (mtm180) cc_final: 0.7325 (mpt180)
REVERT: B   47 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7063 (ttmm)
REVERT: B   73 ASP cc_start: 0.7938 (t70) cc_final: 0.7686 (t70)
REVERT: B  136 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: C   32 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7798 (mm-30)
REVERT: C  136 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7940 (tm-30)
REVERT: C  143 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: D    7 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7572 (mpt180)
REVERT: D   47 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7201 (pttt)
REVERT: D   73 ASP cc_start: 0.7983 (t70) cc_final: 0.7781 (t70)
REVERT: D  123 ASP cc_start: 0.8155 (t0) cc_final: 0.7925 (t0)
REVERT: D  136 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7805 (tm-30)
REVERT: D  146 MET cc_start: 0.8226 (tmm) cc_final: 0.7929 (tmm)
REVERT: E    6 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8043 (mm-30)
REVERT: E    7 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7354 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7257 (pttt)
REVERT: E  136 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: F    7 ARG cc_start: 0.7802 (mtm180) cc_final: 0.7431 (mpt180)
REVERT: F   47 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7107 (ttmt)
REVERT: F  136 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: F  169 GLU cc_start: 0.8380 (tp30) cc_final: 0.8158 (tt0)
REVERT: G    6 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: G    7 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7209 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: H    7 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7570 (mpt180)
REVERT: H   47 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7234 (pttt)
REVERT: H   67 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8765 (mm)
REVERT: H   82 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: H  136 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: H  142 MET cc_start: 0.9332 (tpp) cc_final: 0.9097 (tpt)
REVERT: H  146 MET cc_start: 0.8220 (tmm) cc_final: 0.7937 (tmm)
REVERT: H  155 GLU cc_start: 0.7856 (tt0) cc_final: 0.7619 (tt0)
  outliers start: 25
  outliers final: 12
  residues processed: 236
  average time/residue: 0.1006
  time to fit residues: 34.0962
Evaluate side-chains
  174 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   35 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   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Chi-restraints excluded: chain H residue  192 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 127 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 119 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.136767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.091855 restraints weight = 19491.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.094600 restraints weight = 11561.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.096412 restraints weight = 8351.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.097498 restraints weight = 6853.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.098307 restraints weight = 6091.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12528  Z= 0.184
  Angle     :  0.540   8.379  16888  Z= 0.286
  Chirality :  0.033   0.145   1936
  Planarity :  0.003   0.025   2152
  Dihedral  :  3.351  13.114   1688
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.75 (0.20), residues: 1576
  helix:  2.74 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.61 (0.67), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 177 
 PHE   0.015   0.001   PHE H  27 
 TRP   0.013   0.002   TRP C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12528)
  covalent geometry    : angle       0.54035 (16888)
  hydrogen bonds       : bond        0.04944 ( 1273)
  hydrogen bonds       : angle       3.57506 ( 3819)

*********************** 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
  214 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 181
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: B    7 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7357 (mpt180)
REVERT: B   32 GLU cc_start: 0.8358 (pt0) cc_final: 0.8053 (pt0)
REVERT: B   47 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7027 (ttmm)
REVERT: B   67 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8825 (mm)
REVERT: B   73 ASP cc_start: 0.7983 (t70) cc_final: 0.7693 (t70)
REVERT: B  136 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: B  143 GLU cc_start: 0.8448 (tp30) cc_final: 0.8189 (tm-30)
REVERT: C   32 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: C  136 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: C  143 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: C  155 GLU cc_start: 0.7875 (tt0) cc_final: 0.7640 (tt0)
REVERT: D    7 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7524 (mmp-170)
REVERT: D   47 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7072 (pttt)
REVERT: D   67 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: D   73 ASP cc_start: 0.8002 (t70) cc_final: 0.7788 (t70)
REVERT: D  136 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: D  146 MET cc_start: 0.8267 (tmm) cc_final: 0.7969 (tmm)
REVERT: E    7 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7394 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7067 (ttmt)
REVERT: E  136 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: F    7 ARG cc_start: 0.7802 (mtm180) cc_final: 0.7430 (mpt180)
REVERT: F   47 LYS cc_start: 0.7861 (mmtm) cc_final: 0.6989 (ttmt)
REVERT: F   67 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8840 (mm)
REVERT: F  136 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7883 (tm-30)
REVERT: F  169 GLU cc_start: 0.8414 (tp30) cc_final: 0.8166 (tt0)
REVERT: G    6 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: G    7 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7253 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: H    7 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7496 (mmp-170)
REVERT: H   47 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7089 (pttt)
REVERT: H   67 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8736 (mm)
REVERT: H   82 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: H  136 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: H  146 MET cc_start: 0.8305 (tmm) cc_final: 0.7972 (tmm)
REVERT: H  155 GLU cc_start: 0.7988 (tt0) cc_final: 0.7720 (tt0)
  outliers start: 33
  outliers final: 13
  residues processed: 206
  average time/residue: 0.0949
  time to fit residues: 28.2475
Evaluate side-chains
  174 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
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 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   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  192 ILE
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 64 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 133 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.139485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.094148 restraints weight = 19623.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.097080 restraints weight = 11467.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.099020 restraints weight = 8202.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100335 restraints weight = 6700.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.101120 restraints weight = 5909.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12528  Z= 0.137
  Angle     :  0.505   9.268  16888  Z= 0.266
  Chirality :  0.032   0.218   1936
  Planarity :  0.003   0.023   2152
  Dihedral  :  3.355  12.929   1688
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.23 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.93 (0.20), residues: 1576
  helix:  2.89 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.76 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 177 
 PHE   0.017   0.001   PHE F  27 
 TRP   0.016   0.002   TRP C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12528)
  covalent geometry    : angle       0.50451 (16888)
  hydrogen bonds       : bond        0.04370 ( 1273)
  hydrogen bonds       : angle       3.54176 ( 3819)

*********************** 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
  237 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 193
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7163 (pttt)
REVERT: A  136 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: B    7 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7404 (mpt180)
REVERT: B   47 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7216 (ttmm)
REVERT: B   73 ASP cc_start: 0.7932 (t70) cc_final: 0.7671 (t70)
REVERT: B  136 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: B  143 GLU cc_start: 0.8472 (tp30) cc_final: 0.8174 (tm-30)
REVERT: C   32 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7787 (mm-30)
REVERT: C  136 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: C  143 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: D    7 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7515 (mmp-170)
REVERT: D   47 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7105 (pttt)
REVERT: D   67 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8751 (mm)
REVERT: D   73 ASP cc_start: 0.7884 (t70) cc_final: 0.7614 (t70)
REVERT: D  136 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: E    7 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7398 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7932 (tm-30)
REVERT: F    7 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7446 (mpt180)
REVERT: F   47 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7069 (ttmt)
REVERT: F   67 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: F   73 ASP cc_start: 0.7832 (t70) cc_final: 0.7560 (t70)
REVERT: F  136 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: G    6 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: G    7 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7262 (mmp-170)
REVERT: G   32 GLU cc_start: 0.8167 (pt0) cc_final: 0.7629 (pt0)
REVERT: G  136 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7988 (tm-30)
REVERT: H    7 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7559 (mpt180)
REVERT: H   47 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7255 (pttt)
REVERT: H   67 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8744 (mm)
REVERT: H  136 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7797 (tm-30)
REVERT: H  146 MET cc_start: 0.8215 (tmm) cc_final: 0.7944 (tmm)
REVERT: H  155 GLU cc_start: 0.7901 (tt0) cc_final: 0.7662 (tt0)
  outliers start: 44
  outliers final: 15
  residues processed: 231
  average time/residue: 0.0912
  time to fit residues: 30.6073
Evaluate side-chains
  176 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
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 E residue  197 TRP
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain G residue  192 ILE
Chi-restraints excluded: chain H residue   19 SER
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 24 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 125 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    2.5988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.135655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090418 restraints weight = 19548.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.093133 restraints weight = 11520.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094924 restraints weight = 8329.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.096111 restraints weight = 6869.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.096693 restraints weight = 6119.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12528  Z= 0.196
  Angle     :  0.582   8.156  16888  Z= 0.304
  Chirality :  0.036   0.262   1936
  Planarity :  0.003   0.026   2152
  Dihedral  :  3.389  13.003   1688
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.16 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.74 (0.20), residues: 1576
  helix:  2.76 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.67 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  28 
 PHE   0.015   0.001   PHE F  27 
 TRP   0.021   0.002   TRP G 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (12528)
  covalent geometry    : angle       0.58243 (16888)
  hydrogen bonds       : bond        0.05070 ( 1273)
  hydrogen bonds       : angle       3.63471 ( 3819)

*********************** 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
  197 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7106 (pttt)
REVERT: A  136 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: A  143 GLU cc_start: 0.8421 (tp30) cc_final: 0.8025 (tm-30)
REVERT: B    7 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7411 (mpt180)
REVERT: B   47 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7023 (ttmm)
REVERT: B   67 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8851 (mm)
REVERT: B   73 ASP cc_start: 0.8039 (t70) cc_final: 0.7780 (t70)
REVERT: B  136 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: B  143 GLU cc_start: 0.8446 (tp30) cc_final: 0.8193 (tm-30)
REVERT: C   32 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7766 (mm-30)
REVERT: C  136 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: C  143 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: D    7 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7530 (mmp-170)
REVERT: D   47 LYS cc_start: 0.7710 (mmtm) cc_final: 0.6819 (ttmt)
REVERT: D   67 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8767 (mm)
REVERT: D   73 ASP cc_start: 0.7975 (t70) cc_final: 0.7713 (t70)
REVERT: D  136 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: E    7 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7424 (mmp-170)
REVERT: E   73 ASP cc_start: 0.7812 (t70) cc_final: 0.7604 (t70)
REVERT: E  136 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: E  143 GLU cc_start: 0.8414 (tp30) cc_final: 0.8115 (tm-30)
REVERT: F    7 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7505 (mpt180)
REVERT: F   67 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8829 (mm)
REVERT: F  136 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: G    6 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8057 (mm-30)
REVERT: G    7 ARG cc_start: 0.7690 (mtm180) cc_final: 0.7322 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: G  143 GLU cc_start: 0.8412 (tp30) cc_final: 0.7950 (tm-30)
REVERT: H    7 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7527 (mmp-170)
REVERT: H   67 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8723 (mm)
REVERT: H  136 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7876 (tm-30)
REVERT: H  143 GLU cc_start: 0.8435 (tp30) cc_final: 0.8178 (tm-30)
REVERT: H  146 MET cc_start: 0.8283 (tmm) cc_final: 0.8011 (tmm)
REVERT: H  155 GLU cc_start: 0.7937 (tt0) cc_final: 0.7720 (tt0)
  outliers start: 35
  outliers final: 19
  residues processed: 194
  average time/residue: 0.0961
  time to fit residues: 27.4562
Evaluate side-chains
  183 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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   96 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain C residue  197 TRP
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 E residue  197 TRP
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  192 ILE
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   96 SER
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 75 optimal weight:    0.6980
   chunk 149 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 78 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.140766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.096553 restraints weight = 19405.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.099459 restraints weight = 11340.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.101239 restraints weight = 8102.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102616 restraints weight = 6630.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.103415 restraints weight = 5859.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12528  Z= 0.137
  Angle     :  0.523   8.652  16888  Z= 0.273
  Chirality :  0.034   0.320   1936
  Planarity :  0.003   0.022   2152
  Dihedral  :  3.391  12.719   1688
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.67 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.91 (0.20), residues: 1576
  helix:  2.87 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.69 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  28 
 PHE   0.014   0.001   PHE H  27 
 TRP   0.019   0.002   TRP G 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12528)
  covalent geometry    : angle       0.52331 (16888)
  hydrogen bonds       : bond        0.04329 ( 1273)
  hydrogen bonds       : angle       3.57762 ( 3819)

*********************** 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
  207 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A  143 GLU cc_start: 0.8372 (tp30) cc_final: 0.7819 (tm-30)
REVERT: B    7 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7506 (mpt180)
REVERT: B   47 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7177 (ttmm)
REVERT: B   67 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8823 (mm)
REVERT: B   73 ASP cc_start: 0.7889 (t70) cc_final: 0.7641 (t70)
REVERT: B  136 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7832 (tm-30)
REVERT: B  143 GLU cc_start: 0.8465 (tp30) cc_final: 0.8170 (tm-30)
REVERT: C   32 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7837 (mm-30)
REVERT: C  136 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: C  143 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: D    7 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7542 (mmp-170)
REVERT: D   47 LYS cc_start: 0.7761 (mmtm) cc_final: 0.6959 (ttmt)
REVERT: D   67 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8755 (mm)
REVERT: D   73 ASP cc_start: 0.7847 (t70) cc_final: 0.7574 (t70)
REVERT: D  136 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7846 (tm-30)
REVERT: E    7 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7401 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7126 (ttmt)
REVERT: E  136 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: E  143 GLU cc_start: 0.8404 (tp30) cc_final: 0.7834 (tm-30)
REVERT: F    7 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7526 (mpt180)
REVERT: F   47 LYS cc_start: 0.7665 (mmtm) cc_final: 0.6881 (ttmt)
REVERT: F   67 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8785 (mm)
REVERT: F  136 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: G    7 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7332 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7188 (ttmt)
REVERT: G  136 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: G  143 GLU cc_start: 0.8367 (tp30) cc_final: 0.7853 (tm-30)
REVERT: H    7 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7577 (mpt180)
REVERT: H   47 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7023 (ttmt)
REVERT: H   67 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8730 (mm)
REVERT: H  136 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: H  155 GLU cc_start: 0.7861 (tt0) cc_final: 0.7632 (tt0)
  outliers start: 24
  outliers final: 15
  residues processed: 203
  average time/residue: 0.0886
  time to fit residues: 26.2642
Evaluate side-chains
  177 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
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 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   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  192 ILE
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   96 SER
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 30 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 144 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.141521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.097530 restraints weight = 19280.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.100428 restraints weight = 11268.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102372 restraints weight = 8064.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103668 restraints weight = 6570.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.104204 restraints weight = 5797.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12528  Z= 0.132
  Angle     :  0.529   9.526  16888  Z= 0.276
  Chirality :  0.034   0.303   1936
  Planarity :  0.002   0.021   2152
  Dihedral  :  3.367  12.480   1688
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.02 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.98 (0.20), residues: 1576
  helix:  2.88 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.43 (0.62), residues: 112

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12528)
  covalent geometry    : angle       0.52866 (16888)
  hydrogen bonds       : bond        0.04309 ( 1273)
  hydrogen bonds       : angle       3.54743 ( 3819)

*********************** 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
  213 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: B    7 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7448 (mpt180)
REVERT: B   47 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7212 (ttmt)
REVERT: B   67 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8837 (mm)
REVERT: B   73 ASP cc_start: 0.7872 (t70) cc_final: 0.7623 (t70)
REVERT: B  136 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: B  143 GLU cc_start: 0.8474 (tp30) cc_final: 0.8093 (tm-30)
REVERT: C   32 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7886 (mm-30)
REVERT: C  136 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: C  143 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: D    7 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7465 (mmp-170)
REVERT: D   47 LYS cc_start: 0.7727 (mmtm) cc_final: 0.6907 (ttmt)
REVERT: D   67 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8784 (mm)
REVERT: D   73 ASP cc_start: 0.7782 (t70) cc_final: 0.7513 (t70)
REVERT: D  136 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: E    7 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7508 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7147 (pttt)
REVERT: E  136 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: F    7 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7542 (mpt180)
REVERT: F   47 LYS cc_start: 0.7621 (mmtm) cc_final: 0.6843 (ttmt)
REVERT: F   67 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8763 (mm)
REVERT: F  136 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7762 (tm-30)
REVERT: G    7 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7318 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7096 (ttmt)
REVERT: G  136 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: H    7 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7465 (mmp-170)
REVERT: H   10 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: H   47 LYS cc_start: 0.7669 (mmtm) cc_final: 0.6881 (ttmt)
REVERT: H   67 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8745 (mm)
REVERT: H  136 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7778 (tm-30)
REVERT: H  155 GLU cc_start: 0.7862 (tt0) cc_final: 0.7632 (tt0)
  outliers start: 22
  outliers final: 16
  residues processed: 208
  average time/residue: 0.0860
  time to fit residues: 26.7780
Evaluate side-chains
  187 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
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 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 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  192 ILE
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   96 SER
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 4 optimal weight:    9.9990
   chunk 150 optimal weight:    0.0070
   chunk 64 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    1.4004

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.139089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094099 restraints weight = 19522.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.096980 restraints weight = 11413.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.098891 restraints weight = 8198.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.100117 restraints weight = 6702.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.100894 restraints weight = 5955.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3825

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= 0.147
  Angle     :  0.574  16.106  16888  Z= 0.294
  Chirality :  0.035   0.311   1936
  Planarity :  0.003   0.022   2152
  Dihedral  :  3.369  12.846   1688
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.61 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.98 (0.20), residues: 1576
  helix:  2.92 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.72 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  28 
 PHE   0.024   0.002   PHE F  27 
 TRP   0.018   0.002   TRP C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12528)
  covalent geometry    : angle       0.57421 (16888)
  hydrogen bonds       : bond        0.04478 ( 1273)
  hydrogen bonds       : angle       3.56668 ( 3819)

********************** 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
  194 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: B    7 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7428 (mpt180)
REVERT: B   47 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7074 (ttmt)
REVERT: B   67 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8822 (mm)
REVERT: B   73 ASP cc_start: 0.7949 (t70) cc_final: 0.7679 (t70)
REVERT: B  136 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: B  143 GLU cc_start: 0.8492 (tp30) cc_final: 0.8118 (tm-30)
REVERT: C   32 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7910 (mm-30)
REVERT: C  136 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7927 (tm-30)
REVERT: C  143 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7525 (tm-30)
REVERT: D    7 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7515 (mmp-170)
REVERT: D   10 GLU cc_start: 0.6875 (tp30) cc_final: 0.6474 (tm-30)
REVERT: D   47 LYS cc_start: 0.7625 (mmtm) cc_final: 0.6958 (pttt)
REVERT: D   67 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: D   73 ASP cc_start: 0.7851 (t70) cc_final: 0.7559 (t70)
REVERT: D  136 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: E    7 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7500 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7242 (pttt)
REVERT: E  136 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: F    7 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7502 (mpt180)
REVERT: F   10 GLU cc_start: 0.6847 (tp30) cc_final: 0.6447 (tm-30)
REVERT: F   47 LYS cc_start: 0.7607 (mmtm) cc_final: 0.6792 (ttmt)
REVERT: F   67 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8810 (mm)
REVERT: F  136 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: G    7 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7321 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: H    7 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7419 (mmp-170)
REVERT: H   47 LYS cc_start: 0.7577 (mmtm) cc_final: 0.6945 (pttt)
REVERT: H   67 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: H  136 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: H  155 GLU cc_start: 0.7834 (tt0) cc_final: 0.7602 (tt0)
  outliers start: 21
  outliers final: 16
  residues processed: 190
  average time/residue: 0.0856
  time to fit residues: 24.0260
Evaluate side-chains
  186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
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 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 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  192 ILE
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   96 SER
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 87 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0670
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.8920

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.141469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.097733 restraints weight = 19215.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.100623 restraints weight = 11308.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102536 restraints weight = 8106.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.103701 restraints weight = 6614.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.104473 restraints weight = 5867.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12528  Z= 0.133
  Angle     :  0.559  16.775  16888  Z= 0.285
  Chirality :  0.034   0.320   1936
  Planarity :  0.002   0.020   2152
  Dihedral  :  3.360  12.660   1688
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.61 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.03 (0.20), residues: 1576
  helix:  2.95 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.63 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  28 
 PHE   0.023   0.001   PHE F  27 
 TRP   0.015   0.002   TRP C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12528)
  covalent geometry    : angle       0.55860 (16888)
  hydrogen bonds       : bond        0.04267 ( 1273)
  hydrogen bonds       : angle       3.54745 ( 3819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1689.69 seconds
wall clock time: 29 minutes 52.92 seconds (1792.92 seconds total)