Starting phenix.real_space_refine
on Mon Dec 30 03:22:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6q_28888/12_2024/8f6q_28888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6q_28888/12_2024/8f6q_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_28888/12_2024/8f6q_28888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6q_28888/12_2024/8f6q_28888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6q_28888/12_2024/8f6q_28888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6q_28888/12_2024/8f6q_28888.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    7936      2.51       5
     N    2120      2.21       5
     O    2280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 12352
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1544
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 3, 'TRANS': 195}
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 3.68, per 1000 atoms: 0.30
  Number of scatterers: 12352
  At special positions: 0
  Unit cell: (135.763, 135.763, 53.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    2280      8.00
     N    2120      7.00
     C    7936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.61
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      98.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 22
    Processing helix  chain 'A' and resid 24 through 48
    Processing helix  chain 'A' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 149
    Processing helix  chain 'A' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 199
    Processing helix  chain 'B' and resid 2 through 22
    Processing helix  chain 'B' and resid 24 through 48
    Processing helix  chain 'B' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL B  54 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 149
    Processing helix  chain 'B' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 199
    Processing helix  chain 'C' and resid 2 through 22
    Processing helix  chain 'C' and resid 24 through 48
    Processing helix  chain 'C' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL C  54 " --> pdb=" O   ASP C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS C  79 " --> pdb=" O   GLU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 149
    Processing helix  chain 'C' and resid 151 through 172
      removed outlier: 3.782A  pdb=" N   GLU C 155 " --> pdb=" O   PRO C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 199
    Processing helix  chain 'D' and resid 2 through 22
    Processing helix  chain 'D' and resid 24 through 48
    Processing helix  chain 'D' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL D  54 " --> pdb=" O   ASP D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS D  79 " --> pdb=" O   GLU D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 149
    Processing helix  chain 'D' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU D 155 " --> pdb=" O   PRO D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 199
    Processing helix  chain 'E' and resid 2 through 22
    Processing helix  chain 'E' and resid 24 through 48
    Processing helix  chain 'E' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL E  54 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 99
      removed outlier: 4.140A  pdb=" N   LYS E  79 " --> pdb=" O   GLU E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL E 104 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 149
    Processing helix  chain 'E' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU E 155 " --> pdb=" O   PRO E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 199
    Processing helix  chain 'F' and resid 2 through 22
    Processing helix  chain 'F' and resid 24 through 48
    Processing helix  chain 'F' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL F  54 " --> pdb=" O   ASP F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS F  79 " --> pdb=" O   GLU F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL F 104 " --> pdb=" O   ASP F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 123 through 149
    Processing helix  chain 'F' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU F 155 " --> pdb=" O   PRO F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 173 through 199
    Processing helix  chain 'G' and resid 2 through 22
    Processing helix  chain 'G' and resid 24 through 48
    Processing helix  chain 'G' and resid 50 through 72
      removed outlier: 4.070A  pdb=" N   VAL G  54 " --> pdb=" O   ASP G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 73 through 99
      removed outlier: 4.139A  pdb=" N   LYS G  79 " --> pdb=" O   GLU G  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 122
      removed outlier: 3.927A  pdb=" N   VAL G 104 " --> pdb=" O   ASP G 100 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 123 through 149
    Processing helix  chain 'G' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU G 155 " --> pdb=" O   PRO G 151 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 173 through 199
    Processing helix  chain 'H' and resid 2 through 22
    Processing helix  chain 'H' and resid 24 through 48
    Processing helix  chain 'H' and resid 50 through 72
      removed outlier: 4.071A  pdb=" N   VAL H  54 " --> pdb=" O   ASP H  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 99
      removed outlier: 4.140A  pdb=" N   LYS H  79 " --> pdb=" O   GLU H  75 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 122
      removed outlier: 3.926A  pdb=" N   VAL H 104 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 123 through 149
    Processing helix  chain 'H' and resid 151 through 172
      removed outlier: 3.781A  pdb=" N   GLU H 155 " --> pdb=" O   PRO H 151 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 173 through 199

    1273 hydrogen bonds defined for protein.
    3819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 3.97 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: 0.00
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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.510
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.850
-------------------------------------------------------------------------------
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= 0.395
  Angle     :  0.724  15.844  16888  Z= 0.418
  Chirality :  0.040   0.232   1936
  Planarity :  0.003   0.028   2152
  Dihedral  : 12.978  89.081   4664
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 20.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.19), residues: 1576
  helix:  0.67 (0.12), residues: 1480
  sheet:  None (None), residues: 0
  loop : -3.60 (0.55), residues: 96

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

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

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 362
  time to evaluate  : 1.301 
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: 0.3950
  time to fit residues: 180.6417
Evaluate side-chains
  161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0270
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 138 optimal weight:    4.9990
   overall best weight:    1.5842

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12528  Z= 0.228
  Angle     :  0.542   8.658  16888  Z= 0.283
  Chirality :  0.032   0.153   1936
  Planarity :  0.003   0.029   2152
  Dihedral  :  3.429  13.184   1688
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.63 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.20), residues: 1576
  helix:  2.09 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -2.19 (0.60), residues: 104

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

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

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 215
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7275 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7844 (tm-30)
REVERT: B    6 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7419 (mm-30)
REVERT: B    7 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7200 (mmp-170)
REVERT: B   24 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: B   47 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7260 (ttmm)
REVERT: B   48 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7265 (mm-30)
REVERT: B  136 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: C  136 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: C  142 MET cc_start: 0.9103 (tpp) cc_final: 0.8848 (tpt)
REVERT: D    4 ILE cc_start: 0.7942 (mm) cc_final: 0.7727 (tt)
REVERT: D    7 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7514 (mpt180)
REVERT: D  136 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7723 (tm-30)
REVERT: D  142 MET cc_start: 0.9103 (tpp) cc_final: 0.8535 (tpt)
REVERT: E    6 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: E    7 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7255 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: E  142 MET cc_start: 0.9203 (tpp) cc_final: 0.8853 (tpt)
REVERT: F    6 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7425 (mm-30)
REVERT: F    7 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7368 (mmp-170)
REVERT: F   47 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7320 (ttmt)
REVERT: F  136 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: G    6 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: G    7 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7096 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: G  192 ILE cc_start: 0.8697 (tt) cc_final: 0.8366 (tt)
REVERT: H    4 ILE cc_start: 0.7927 (mm) cc_final: 0.7718 (tt)
REVERT: H    7 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7476 (mpt180)
REVERT: H  136 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: H  142 MET cc_start: 0.9150 (tpp) cc_final: 0.8580 (tpt)
REVERT: H  169 GLU cc_start: 0.8323 (tp30) cc_final: 0.8102 (tt0)
REVERT: H  192 ILE cc_start: 0.8850 (tt) cc_final: 0.8544 (tt)
  outliers start: 22
  outliers final: 9
  residues processed: 230
  average time/residue: 0.2533
  time to fit residues: 82.8616
Evaluate side-chains
  167 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 158
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
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 76 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 114 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 138 optimal weight:    7.9990
   chunk 149 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   overall best weight:    2.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2808

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= 0.279
  Angle     :  0.553   6.698  16888  Z= 0.290
  Chirality :  0.032   0.119   1936
  Planarity :  0.003   0.028   2152
  Dihedral  :  3.383  13.224   1688
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 11.06 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.39 (0.20), residues: 1576
  helix:  2.53 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -2.07 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 197 
 PHE   0.012   0.001   PHE G 183 
 ARG   0.003   0.000   ARG C 177 

*********************** 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
  227 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 1.512 
Fit side-chains
REVERT: A    7 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7374 (mmp-170)
REVERT: A  136 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7844 (tm-30)
REVERT: B    7 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7264 (mmp-170)
REVERT: B   47 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7321 (ttmt)
REVERT: B   73 ASP cc_start: 0.8076 (t70) cc_final: 0.7866 (t70)
REVERT: B  132 GLU cc_start: 0.7867 (tp30) cc_final: 0.7630 (tp30)
REVERT: B  136 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: C  136 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: C  142 MET cc_start: 0.9152 (tpp) cc_final: 0.8652 (tpt)
REVERT: C  143 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: D    7 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7545 (mpt180)
REVERT: D  136 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: D  142 MET cc_start: 0.9048 (tpp) cc_final: 0.8514 (tpt)
REVERT: D  146 MET cc_start: 0.8230 (tmm) cc_final: 0.7864 (tmm)
REVERT: E    6 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: E    7 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7328 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7068 (ttmt)
REVERT: E  136 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: F    7 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7481 (mpt180)
REVERT: F  136 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: G    6 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: G    7 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7160 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7696 (mmtm) cc_final: 0.7103 (ttmt)
REVERT: G  136 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: H    7 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7488 (mpt180)
REVERT: H  136 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: H  142 MET cc_start: 0.9156 (tpp) cc_final: 0.8457 (tpt)
REVERT: H  155 GLU cc_start: 0.7917 (tt0) cc_final: 0.7638 (tt0)
REVERT: H  169 GLU cc_start: 0.8414 (tp30) cc_final: 0.8192 (tt0)
  outliers start: 39
  outliers final: 9
  residues processed: 218
  average time/residue: 0.2438
  time to fit residues: 76.4442
Evaluate side-chains
  162 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 138 optimal weight:    5.9990
   chunk 146 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0070
   chunk 131 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.8006

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12528  Z= 0.235
  Angle     :  0.504   7.271  16888  Z= 0.268
  Chirality :  0.032   0.111   1936
  Planarity :  0.003   0.026   2152
  Dihedral  :  3.370  13.372   1688
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.78 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.78 (0.20), residues: 1576
  helix:  2.77 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.78 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G 197 
 PHE   0.010   0.001   PHE C  27 
 ARG   0.003   0.000   ARG C 177 

*********************** 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
  218 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 1.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: B    7 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7344 (mpt180)
REVERT: B   47 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7292 (ttmt)
REVERT: B  136 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: C   32 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7840 (mm-30)
REVERT: C  136 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: C  142 MET cc_start: 0.9157 (tpp) cc_final: 0.8832 (tpt)
REVERT: C  143 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: D    7 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7576 (mpt180)
REVERT: D   47 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7101 (pttt)
REVERT: D  136 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: D  146 MET cc_start: 0.8276 (tmm) cc_final: 0.7920 (tmm)
REVERT: E    6 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: E    7 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7300 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7816 (mmtm) cc_final: 0.7145 (ttmt)
REVERT: E  136 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: F    7 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7429 (mpt180)
REVERT: F   47 LYS cc_start: 0.7743 (mmtm) cc_final: 0.6990 (ttmt)
REVERT: F  136 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: G    6 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8061 (mm-30)
REVERT: G    7 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7193 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7294 (ttmt)
REVERT: G  136 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: G  155 GLU cc_start: 0.7769 (tt0) cc_final: 0.7540 (tt0)
REVERT: H    7 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7565 (mpt180)
REVERT: H   47 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7067 (pttt)
REVERT: H   67 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8861 (mm)
REVERT: H   82 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: H  136 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: H  142 MET cc_start: 0.9231 (tpp) cc_final: 0.8532 (tpt)
REVERT: H  146 MET cc_start: 0.8254 (tmm) cc_final: 0.7915 (tmm)
REVERT: H  155 GLU cc_start: 0.7911 (tt0) cc_final: 0.7623 (tt0)
  outliers start: 27
  outliers final: 13
  residues processed: 212
  average time/residue: 0.2557
  time to fit residues: 76.5526
Evaluate side-chains
  166 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
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 B residue  189 ILE
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 G residue  192 ILE
Chi-restraints excluded: chain G residue  197 TRP
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.3382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3363

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= 0.203
  Angle     :  0.495   8.731  16888  Z= 0.263
  Chirality :  0.031   0.109   1936
  Planarity :  0.003   0.024   2152
  Dihedral  :  3.355  13.113   1688
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.71 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.03 (0.20), residues: 1576
  helix:  2.93 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.66 (0.64), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 197 
 PHE   0.017   0.001   PHE F  27 
 ARG   0.005   0.000   ARG G  28 

*********************** 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
  230 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 197
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: B    7 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7400 (mpt180)
REVERT: B   47 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7425 (ttmt)
REVERT: B  136 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: C  136 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: C  143 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: D    7 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7590 (mpt180)
REVERT: D   47 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7095 (pttt)
REVERT: D  136 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: D  146 MET cc_start: 0.8207 (tmm) cc_final: 0.7922 (tmm)
REVERT: E    7 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7408 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7335 (pttt)
REVERT: E  136 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: F    7 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7440 (mpt180)
REVERT: F   47 LYS cc_start: 0.7806 (mmtm) cc_final: 0.7026 (ttmt)
REVERT: F  136 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: G    6 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: G    7 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7222 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7393 (pttt)
REVERT: G  136 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: H    7 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7562 (mpt180)
REVERT: H   47 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7112 (pttt)
REVERT: H   67 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8850 (mm)
REVERT: H   82 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7811 (mm-30)
REVERT: H  136 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: H  142 MET cc_start: 0.9275 (tpp) cc_final: 0.8533 (tpt)
REVERT: H  146 MET cc_start: 0.8245 (tmm) cc_final: 0.7955 (tmm)
REVERT: H  155 GLU cc_start: 0.7933 (tt0) cc_final: 0.7654 (tt0)
  outliers start: 33
  outliers final: 15
  residues processed: 226
  average time/residue: 0.2468
  time to fit residues: 80.7610
Evaluate side-chains
  178 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
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  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  170 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 132 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 147 optimal weight:    3.9990
   chunk 122 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3563

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= 0.196
  Angle     :  0.508   9.257  16888  Z= 0.267
  Chirality :  0.032   0.148   1936
  Planarity :  0.003   0.022   2152
  Dihedral  :  3.310  12.465   1688
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.06 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.09 (0.20), residues: 1576
  helix:  2.99 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.72 (0.61), residues: 120

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

*********************** 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
  241 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 199
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6921 (tm-30)
REVERT: A  136 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: A  142 MET cc_start: 0.9196 (tpp) cc_final: 0.8990 (mmm)
REVERT: B    7 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7444 (mpt180)
REVERT: B   67 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8897 (mm)
REVERT: B  136 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: C  136 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: C  143 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: D    7 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7557 (mpt180)
REVERT: D   24 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6895 (tm-30)
REVERT: D   47 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7117 (pttt)
REVERT: D   67 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8816 (mm)
REVERT: D  136 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: D  146 MET cc_start: 0.8135 (tmm) cc_final: 0.7929 (tmm)
REVERT: E    7 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7372 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7206 (ttmt)
REVERT: E  136 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: F    7 ARG cc_start: 0.7802 (mtm180) cc_final: 0.7459 (mpt180)
REVERT: F   47 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7046 (ttmt)
REVERT: F   67 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8913 (mm)
REVERT: F   73 ASP cc_start: 0.7818 (t70) cc_final: 0.7547 (t70)
REVERT: F  136 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: G    6 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8055 (mm-30)
REVERT: G    7 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7260 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7750 (mmtm) cc_final: 0.7390 (pttt)
REVERT: G  136 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7842 (tm-30)
REVERT: H    7 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7538 (mpt180)
REVERT: H   47 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7142 (pttt)
REVERT: H   67 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8876 (mm)
REVERT: H   82 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: H  136 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: H  142 MET cc_start: 0.9280 (tpp) cc_final: 0.9001 (tpt)
REVERT: H  146 MET cc_start: 0.8284 (tmm) cc_final: 0.7975 (tmm)
REVERT: H  155 GLU cc_start: 0.7929 (tt0) cc_final: 0.7649 (tt0)
  outliers start: 42
  outliers final: 13
  residues processed: 235
  average time/residue: 0.2391
  time to fit residues: 81.2446
Evaluate side-chains
  180 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 163
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
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   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   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 141 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3623

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= 0.205
  Angle     :  0.525   8.411  16888  Z= 0.276
  Chirality :  0.033   0.265   1936
  Planarity :  0.003   0.020   2152
  Dihedral  :  3.336  13.493   1688
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.07 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.07 (0.20), residues: 1576
  helix:  2.98 (0.12), residues: 1456
  sheet:  None (None), residues: 0
  loop : -1.66 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 197 
 PHE   0.022   0.001   PHE F  27 
 ARG   0.003   0.000   ARG E  28 

*********************** 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
  216 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.7778 (t70) cc_final: 0.7576 (t70)
REVERT: A  136 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7803 (tm-30)
REVERT: B    7 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7475 (mpt180)
REVERT: B   47 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7039 (ttmm)
REVERT: B   67 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8886 (mm)
REVERT: B  136 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: C  136 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: C  143 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: D    7 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7542 (mpt180)
REVERT: D   47 LYS cc_start: 0.7752 (mmtm) cc_final: 0.6827 (ttmm)
REVERT: D   67 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8798 (mm)
REVERT: D  136 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: E    7 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7458 (mmp-170)
REVERT: E   10 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6567 (tp30)
REVERT: E   47 LYS cc_start: 0.7852 (mmtm) cc_final: 0.7221 (ttmt)
REVERT: E  136 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: F    7 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7475 (mpt180)
REVERT: F   47 LYS cc_start: 0.7794 (mmtm) cc_final: 0.6965 (ttmt)
REVERT: F   67 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8924 (mm)
REVERT: F  136 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: G    6 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: G    7 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7281 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7248 (ttmt)
REVERT: G  136 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: H    7 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7531 (mpt180)
REVERT: H   47 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7143 (pttt)
REVERT: H   67 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8877 (mm)
REVERT: H   82 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7734 (mm-30)
REVERT: H  136 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7681 (tm-30)
REVERT: H  142 MET cc_start: 0.9278 (tpp) cc_final: 0.8997 (tpt)
REVERT: H  146 MET cc_start: 0.8289 (tmm) cc_final: 0.7979 (tmm)
REVERT: H  155 GLU cc_start: 0.7928 (tt0) cc_final: 0.7644 (tt0)
  outliers start: 32
  outliers final: 18
  residues processed: 211
  average time/residue: 0.2258
  time to fit residues: 69.9616
Evaluate side-chains
  186 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain G residue  197 TRP
Chi-restraints excluded: chain H residue   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 58 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 133 optimal weight:   10.0000
   chunk 140 optimal weight:    0.0570
   overall best weight:    1.1504

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12528  Z= 0.194
  Angle     :  0.531   9.354  16888  Z= 0.279
  Chirality :  0.035   0.317   1936
  Planarity :  0.003   0.021   2152
  Dihedral  :  3.375  12.603   1688
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.92 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.01 (0.20), residues: 1576
  helix:  2.90 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.40 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 197 
 PHE   0.023   0.001   PHE F  27 
 ARG   0.003   0.000   ARG E  28 

*********************** 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
  216 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: B    7 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7405 (mpt180)
REVERT: B   10 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6591 (tm-30)
REVERT: B   47 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7024 (ttmm)
REVERT: B   67 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8879 (mm)
REVERT: B  136 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7753 (tm-30)
REVERT: C  136 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: C  143 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7571 (tm-30)
REVERT: D    7 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7539 (mpt180)
REVERT: D   47 LYS cc_start: 0.7746 (mmtm) cc_final: 0.6836 (ttmm)
REVERT: D   67 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8819 (mm)
REVERT: D  136 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: E    7 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7455 (mmp-170)
REVERT: E  136 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: F    7 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7493 (mpt180)
REVERT: F   47 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7000 (ttmt)
REVERT: F   67 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8925 (mm)
REVERT: F  136 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: G    6 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: G    7 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7312 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: H    7 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7544 (mpt180)
REVERT: H   47 LYS cc_start: 0.7708 (mmtm) cc_final: 0.6916 (ttmt)
REVERT: H   67 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8852 (mm)
REVERT: H  136 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: H  142 MET cc_start: 0.9287 (tpp) cc_final: 0.8991 (tpt)
REVERT: H  146 MET cc_start: 0.8256 (tmm) cc_final: 0.7943 (tmm)
REVERT: H  155 GLU cc_start: 0.7944 (tt0) cc_final: 0.7686 (tt0)
REVERT: H  192 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8348 (tp)
  outliers start: 29
  outliers final: 18
  residues processed: 212
  average time/residue: 0.2486
  time to fit residues: 76.7970
Evaluate side-chains
  189 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue  170 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  170 LEU
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
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 H residue   67 LEU
Chi-restraints excluded: chain H residue   96 SER
Chi-restraints excluded: chain H residue  170 LEU
Chi-restraints excluded: chain H residue  192 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.7980
   chunk 136 optimal weight:   10.0000
   chunk 140 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 59 optimal weight:    9.9990
   chunk 107 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9980
   overall best weight:    0.9380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12528  Z= 0.184
  Angle     :  0.539   9.624  16888  Z= 0.280
  Chirality :  0.035   0.326   1936
  Planarity :  0.002   0.019   2152
  Dihedral  :  3.346  13.088   1688
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.76 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.06 (0.20), residues: 1576
  helix:  2.94 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.47 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 197 
 PHE   0.023   0.001   PHE F  27 
 ARG   0.003   0.000   ARG E  28 

*********************** 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
  208 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: B    7 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7392 (mpt180)
REVERT: B   47 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7009 (ttmm)
REVERT: B   67 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8825 (mm)
REVERT: B  136 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: C  136 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: C  143 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7545 (tm-30)
REVERT: D    7 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7542 (mpt180)
REVERT: D   47 LYS cc_start: 0.7704 (mmtm) cc_final: 0.6821 (ttmm)
REVERT: D   67 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8809 (mm)
REVERT: D  136 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: E    7 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7450 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7155 (ttmt)
REVERT: E  136 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7892 (tm-30)
REVERT: F    7 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7448 (mpt180)
REVERT: F   10 GLU cc_start: 0.6860 (tp30) cc_final: 0.6446 (tm-30)
REVERT: F   47 LYS cc_start: 0.7796 (mmtm) cc_final: 0.6976 (ttmt)
REVERT: F   67 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8870 (mm)
REVERT: F  136 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: G    6 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: G    7 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7271 (mmp-170)
REVERT: G   47 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7221 (ttmt)
REVERT: G  136 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7701 (tm-30)
REVERT: H    7 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7447 (mpt180)
REVERT: H   10 GLU cc_start: 0.6871 (tp30) cc_final: 0.6499 (tm-30)
REVERT: H   47 LYS cc_start: 0.7591 (mmtm) cc_final: 0.6792 (ttmt)
REVERT: H  136 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: H  142 MET cc_start: 0.9267 (tpp) cc_final: 0.9019 (tpt)
REVERT: H  146 MET cc_start: 0.8204 (tmm) cc_final: 0.7941 (tmm)
REVERT: H  155 GLU cc_start: 0.7927 (tt0) cc_final: 0.7663 (tt0)
  outliers start: 21
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2368
  time to fit residues: 70.8234
Evaluate side-chains
  189 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue   67 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   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   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 88 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 151 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 12 optimal weight:    0.3980
   chunk 93 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 95 optimal weight:   20.0000
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4010

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= 0.179
  Angle     :  0.560  16.241  16888  Z= 0.287
  Chirality :  0.034   0.310   1936
  Planarity :  0.002   0.020   2152
  Dihedral  :  3.323  12.632   1688
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.68 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.11 (0.20), residues: 1576
  helix:  2.97 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.46 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 197 
 PHE   0.020   0.001   PHE F  27 
 ARG   0.003   0.000   ARG E  28 

********************** 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
  211 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: B    7 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7420 (mpt180)
REVERT: B   47 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7031 (ttmt)
REVERT: B   67 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8869 (mm)
REVERT: B  136 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: C  136 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7853 (tm-30)
REVERT: C  143 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: D    7 ARG cc_start: 0.7858 (mtm180) cc_final: 0.7570 (mpt180)
REVERT: D   10 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6554 (tp30)
REVERT: D   47 LYS cc_start: 0.7674 (mmtm) cc_final: 0.6807 (ttmm)
REVERT: D   67 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8804 (mm)
REVERT: D  136 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: E    7 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7496 (mmp-170)
REVERT: E   47 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7144 (ttmt)
REVERT: E  136 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7886 (tm-30)
REVERT: F    7 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7438 (mmp-170)
REVERT: F   10 GLU cc_start: 0.6832 (tp30) cc_final: 0.6408 (tm-30)
REVERT: F   67 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8913 (mm)
REVERT: F  136 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7822 (tm-30)
REVERT: G    7 ARG cc_start: 0.7683 (mtm180) cc_final: 0.7345 (mmp-170)
REVERT: G  136 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: H    7 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7507 (mmp-170)
REVERT: H   47 LYS cc_start: 0.7647 (mmtm) cc_final: 0.6856 (ttmt)
REVERT: H   67 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8867 (mm)
REVERT: H  136 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: H  142 MET cc_start: 0.9294 (tpp) cc_final: 0.9027 (tpt)
REVERT: H  143 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: H  146 MET cc_start: 0.8190 (tmm) cc_final: 0.7967 (tmm)
REVERT: H  155 GLU cc_start: 0.7880 (tt0) cc_final: 0.7598 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 206
  average time/residue: 0.2445
  time to fit residues: 72.6831
Evaluate side-chains
  192 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain C residue   67 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 D residue  189 ILE
Chi-restraints excluded: chain E residue  170 LEU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain F residue   67 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  170 LEU
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   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 36 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.142015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.097097 restraints weight = 19414.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.100112 restraints weight = 11264.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.102101 restraints weight = 8034.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12528  Z= 0.182
  Angle     :  0.557  16.157  16888  Z= 0.286
  Chirality :  0.034   0.307   1936
  Planarity :  0.002   0.020   2152
  Dihedral  :  3.320  12.593   1688
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.19 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.14 (0.19), residues: 1576
  helix:  2.98 (0.12), residues: 1464
  sheet:  None (None), residues: 0
  loop : -1.43 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 197 
 PHE   0.017   0.001   PHE H 183 
 ARG   0.005   0.000   ARG E 162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2245.24 seconds
wall clock time: 41 minutes 56.18 seconds (2516.18 seconds total)