Starting phenix.real_space_refine
on Sat Aug 23 05:59:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6r_28889/08_2025/8f6r_28889.map"
  }
  resolution = 4.0
  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=   0.003 sd=   0.057
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      12      5.16       5
     C    6348      2.51       5
     N    1872      2.21       5
     O    2058      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  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: 10290
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1715
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 7, 'TRANS': 211}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.33, per 1000 atoms: 0.13
  Number of scatterers: 10290
  At special positions: 0
  Unit cell: (125.073, 129.349, 54.519, 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      12     16.00
     O    2058      8.00
     N    1872      7.00
     C    6348      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: 0.95
  Conformation dependent library (CDL) restraints added in 317.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      96.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 29
    Processing helix  chain 'A' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 85
    Processing helix  chain 'A' and resid 86 through 110
    Processing helix  chain 'A' and resid 113 through 141
    Processing helix  chain 'A' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 197
    Processing helix  chain 'A' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
    Processing helix  chain 'B' and resid 30 through 54
      removed outlier: 4.073A  pdb=" N   LEU B  43 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP B  54 " --> pdb=" O   GLU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 85
    Processing helix  chain 'B' and resid 86 through 110
    Processing helix  chain 'B' and resid 113 through 141
    Processing helix  chain 'B' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN B 166 " --> pdb=" O   GLU B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 197
    Processing helix  chain 'B' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 29
    Processing helix  chain 'C' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU C  43 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP C  54 " --> pdb=" O   GLU C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 85
    Processing helix  chain 'C' and resid 86 through 110
    Processing helix  chain 'C' and resid 113 through 141
    Processing helix  chain 'C' and resid 142 through 166
      removed outlier: 3.543A  pdb=" N   ASN C 166 " --> pdb=" O   GLU C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 197
    Processing helix  chain 'C' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU C 218 " --> pdb=" O   GLU C 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 29
    Processing helix  chain 'D' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU D  43 " --> pdb=" O   GLU D  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP D  54 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 85
    Processing helix  chain 'D' and resid 86 through 110
    Processing helix  chain 'D' and resid 113 through 141
    Processing helix  chain 'D' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN D 166 " --> pdb=" O   GLU D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 197
    Processing helix  chain 'D' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG D 202 " --> pdb=" O   ASP D 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU D 218 " --> pdb=" O   GLU D 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 29
    Processing helix  chain 'E' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU E  43 " --> pdb=" O   GLU E  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP E  54 " --> pdb=" O   GLU E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 85
    Processing helix  chain 'E' and resid 86 through 110
    Processing helix  chain 'E' and resid 113 through 141
    Processing helix  chain 'E' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN E 166 " --> pdb=" O   GLU E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 169 through 197
    Processing helix  chain 'E' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG E 202 " --> pdb=" O   ASP E 198 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU E 218 " --> pdb=" O   GLU E 214 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 29
    Processing helix  chain 'F' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU F  43 " --> pdb=" O   GLU F  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP F  54 " --> pdb=" O   GLU F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 57 through 85
    Processing helix  chain 'F' and resid 86 through 110
    Processing helix  chain 'F' and resid 113 through 141
    Processing helix  chain 'F' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN F 166 " --> pdb=" O   GLU F 162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 197
    Processing helix  chain 'F' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG F 202 " --> pdb=" O   ASP F 198 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU F 218 " --> pdb=" O   GLU F 214 " (cutoff:3.500A)

    1045 hydrogen bonds defined for protein.
    3135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3786
        1.34 -     1.46: 571
        1.46 -     1.57: 5987
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 10368
  Sorted by residual:
  bond pdb=" CB  TRP C  52 "
       pdb=" CG  TRP C  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.447  0.051 3.10e-02 1.04e+03 2.67e+00
  bond pdb=" CB  TRP F  52 "
       pdb=" CG  TRP F  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.64e+00
  bond pdb=" CB  TRP B  52 "
       pdb=" CG  TRP B  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.62e+00
  bond pdb=" CB  TRP E  52 "
       pdb=" CG  TRP E  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.58e+00
  bond pdb=" CB  TRP A  52 "
       pdb=" CG  TRP A  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.57e+00
  ... (remaining 10363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 13621
        1.78 -     3.55: 305
        3.55 -     5.33: 72
        5.33 -     7.11: 24
        7.11 -     8.88: 6
  Bond angle restraints: 14028
  Sorted by residual:
  angle pdb=" N   SER B  58 "
        pdb=" CA  SER B  58 "
        pdb=" C   SER B  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.16   -8.88 1.09e+00 8.42e-01 6.64e+01
  angle pdb=" N   SER A  58 "
        pdb=" CA  SER A  58 "
        pdb=" C   SER A  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.16   -8.88 1.09e+00 8.42e-01 6.63e+01
  angle pdb=" N   SER D  58 "
        pdb=" CA  SER D  58 "
        pdb=" C   SER D  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.14   -8.86 1.09e+00 8.42e-01 6.61e+01
  angle pdb=" N   SER C  58 "
        pdb=" CA  SER C  58 "
        pdb=" C   SER C  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.13   -8.85 1.09e+00 8.42e-01 6.59e+01
  angle pdb=" N   SER F  58 "
        pdb=" CA  SER F  58 "
        pdb=" C   SER F  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.12   -8.84 1.09e+00 8.42e-01 6.58e+01
  ... (remaining 14023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.27: 5694
       13.27 -    26.55: 690
       26.55 -    39.82: 198
       39.82 -    53.10: 42
       53.10 -    66.37: 18
  Dihedral angle restraints: 6642
    sinusoidal: 2754
      harmonic: 3888
  Sorted by residual:
  dihedral pdb=" CA  TRP E  52 "
           pdb=" C   TRP E  52 "
           pdb=" N   LEU E  53 "
           pdb=" CA  LEU E  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  TRP A  52 "
           pdb=" C   TRP A  52 "
           pdb=" N   LEU A  53 "
           pdb=" CA  LEU A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.12  -16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  TRP F  52 "
           pdb=" C   TRP F  52 "
           pdb=" N   LEU F  53 "
           pdb=" CA  LEU F  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1473
       0.061 -    0.122: 164
       0.122 -    0.183: 13
       0.183 -    0.244: 6
       0.244 -    0.305: 6
  Chirality restraints: 1662
  Sorted by residual:
  chirality pdb=" CA  SER B  58 "
            pdb=" N   SER B  58 "
            pdb=" C   SER B  58 "
            pdb=" CB  SER B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  SER F  58 "
            pdb=" N   SER F  58 "
            pdb=" C   SER F  58 "
            pdb=" CB  SER F  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  SER D  58 "
            pdb=" N   SER D  58 "
            pdb=" C   SER D  58 "
            pdb=" CB  SER D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1659 not shown)

  Planarity restraints: 1884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  86 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO C  87 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C  87 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  87 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  86 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO E  87 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO E  87 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  87 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  86 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A  87 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  87 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  87 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1881 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 42
        2.58 -     3.16: 9766
        3.16 -     3.74: 17399
        3.74 -     4.32: 20508
        4.32 -     4.90: 33156
  Nonbonded interactions: 80871
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU F  11 "
            pdb=" NH2 ARG F  15 "
     model   vdw
     1.997 3.120
  nonbonded pdb=" OE2 GLU B  11 "
            pdb=" NH2 ARG B  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU D  11 "
            pdb=" NH2 ARG D  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU C  11 "
            pdb=" NH2 ARG C  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU A  11 "
            pdb=" NH2 ARG A  15 "
     model   vdw
     1.998 3.120
  ... (remaining 80866 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.860
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
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      :  0.005   0.051  10368  Z= 0.240
  Angle     :  0.751   8.883  14028  Z= 0.474
  Chirality :  0.043   0.305   1662
  Planarity :  0.005   0.044   1884
  Dihedral  : 12.985  66.374   4062
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  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: -1.46 (0.20), residues: 1302
  helix: -0.69 (0.13), residues: 1248
  sheet:  None (None), residues: 0
  loop : -2.81 (0.56), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  76 
 PHE   0.002   0.000   PHE B 185 
 TRP   0.010   0.002   TRP C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (10368)
  covalent geometry    : angle       0.75089 (14028)
  hydrogen bonds       : bond        0.08566 ( 1045)
  hydrogen bonds       : angle       4.56979 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  110 ASN cc_start: 0.8677 (m110) cc_final: 0.8269 (t0)
REVERT: A  121 LYS cc_start: 0.9440 (mttt) cc_final: 0.9078 (mtpp)
REVERT: A  142 ASP cc_start: 0.8086 (t0) cc_final: 0.7856 (t0)
REVERT: A  183 ILE cc_start: 0.9127 (mt) cc_final: 0.8831 (tp)
REVERT: B  121 LYS cc_start: 0.9445 (mttt) cc_final: 0.9042 (mtpp)
REVERT: B  142 ASP cc_start: 0.8038 (t0) cc_final: 0.7561 (t0)
REVERT: B  185 PHE cc_start: 0.8784 (t80) cc_final: 0.8562 (t80)
REVERT: C  110 ASN cc_start: 0.8679 (m110) cc_final: 0.8089 (t0)
REVERT: C  121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9041 (mtpt)
REVERT: C  142 ASP cc_start: 0.8128 (t0) cc_final: 0.7719 (t0)
REVERT: C  183 ILE cc_start: 0.9199 (mt) cc_final: 0.8981 (tp)
REVERT: C  185 PHE cc_start: 0.8818 (t80) cc_final: 0.8171 (t80)
REVERT: D   12 GLU cc_start: 0.8658 (tp30) cc_final: 0.8448 (tp30)
REVERT: D  110 ASN cc_start: 0.8653 (m110) cc_final: 0.8405 (m110)
REVERT: D  121 LYS cc_start: 0.9431 (mttt) cc_final: 0.9120 (mtpp)
REVERT: D  183 ILE cc_start: 0.9079 (mt) cc_final: 0.8811 (tp)
REVERT: D  185 PHE cc_start: 0.8747 (t80) cc_final: 0.8460 (t80)
REVERT: E  110 ASN cc_start: 0.8714 (m110) cc_final: 0.8275 (t0)
REVERT: E  121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9132 (mtpp)
REVERT: E  142 ASP cc_start: 0.7971 (t0) cc_final: 0.7522 (t0)
REVERT: E  183 ILE cc_start: 0.9170 (mt) cc_final: 0.8923 (tp)
REVERT: F  110 ASN cc_start: 0.8649 (m110) cc_final: 0.8260 (t0)
REVERT: F  121 LYS cc_start: 0.9451 (mttt) cc_final: 0.9048 (mtpt)
REVERT: F  185 PHE cc_start: 0.9000 (t80) cc_final: 0.8268 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 364
  average time/residue: 0.1006
  time to fit residues: 49.7306
Evaluate side-chains
  205 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0040
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
B 117 ASN
B 173 ASN
** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 173 ASN
D 173 ASN
E 173 ASN
** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 173 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.100288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.077599 restraints weight = 25111.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.081013 restraints weight = 15653.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.083369 restraints weight = 11516.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.084981 restraints weight = 9349.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.086047 restraints weight = 8053.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10368  Z= 0.144
  Angle     :  0.603   9.266  14028  Z= 0.319
  Chirality :  0.040   0.333   1662
  Planarity :  0.005   0.035   1884
  Dihedral  :  3.451  13.215   1458
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.05 %
    Favored  : 84.19 %
  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:  2.15 (0.21), residues: 1302
  helix:  1.66 (0.13), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.74 (0.60), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 165 
 PHE   0.024   0.002   PHE A 185 
 TRP   0.014   0.001   TRP E 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10368)
  covalent geometry    : angle       0.60310 (14028)
  hydrogen bonds       : bond        0.03726 ( 1045)
  hydrogen bonds       : angle       3.50517 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 271
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ASN cc_start: 0.8634 (m110) cc_final: 0.8061 (t0)
REVERT: A  121 LYS cc_start: 0.9377 (mttt) cc_final: 0.9098 (mtpp)
REVERT: A  142 ASP cc_start: 0.8230 (t0) cc_final: 0.7917 (t0)
REVERT: A  152 LEU cc_start: 0.9334 (pp) cc_final: 0.8881 (tp)
REVERT: A  190 LEU cc_start: 0.9285 (mt) cc_final: 0.8987 (mt)
REVERT: B  118 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7885 (mt-10)
REVERT: B  121 LYS cc_start: 0.9378 (mttt) cc_final: 0.9172 (mtpp)
REVERT: B  142 ASP cc_start: 0.7899 (t0) cc_final: 0.7632 (t0)
REVERT: B  164 GLN cc_start: 0.8426 (tt0) cc_final: 0.8163 (tt0)
REVERT: C  110 ASN cc_start: 0.8706 (m110) cc_final: 0.8030 (t0)
REVERT: C  121 LYS cc_start: 0.9358 (mttt) cc_final: 0.9088 (mtpt)
REVERT: C  142 ASP cc_start: 0.8151 (t0) cc_final: 0.7918 (t0)
REVERT: D   58 SER cc_start: 0.8658 (m) cc_final: 0.8238 (p)
REVERT: D  110 ASN cc_start: 0.8498 (m110) cc_final: 0.7892 (t0)
REVERT: D  121 LYS cc_start: 0.9380 (mttt) cc_final: 0.9107 (mtpp)
REVERT: D  152 LEU cc_start: 0.9294 (pp) cc_final: 0.8902 (tp)
REVERT: E  110 ASN cc_start: 0.8623 (m110) cc_final: 0.8081 (t0)
REVERT: E  142 ASP cc_start: 0.7980 (t0) cc_final: 0.7700 (t0)
REVERT: E  152 LEU cc_start: 0.9333 (pp) cc_final: 0.8895 (tp)
REVERT: E  164 GLN cc_start: 0.8435 (tt0) cc_final: 0.8172 (tt0)
REVERT: F  110 ASN cc_start: 0.8691 (m110) cc_final: 0.8057 (t0)
REVERT: F  121 LYS cc_start: 0.9381 (mttt) cc_final: 0.9073 (mtpt)
REVERT: F  185 PHE cc_start: 0.8696 (t80) cc_final: 0.8226 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 286
  average time/residue: 0.0777
  time to fit residues: 31.8547
Evaluate side-chains
  234 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 214
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   59 ASP
Chi-restraints excluded: chain E residue  107 VAL
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  180 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
D 164 GLN
F 164 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.076993 restraints weight = 25230.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.080137 restraints weight = 16270.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.082361 restraints weight = 12222.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.083922 restraints weight = 9987.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.084842 restraints weight = 8667.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10368  Z= 0.153
  Angle     :  0.593   9.852  14028  Z= 0.314
  Chirality :  0.039   0.375   1662
  Planarity :  0.004   0.031   1884
  Dihedral  :  3.421  13.155   1458
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.38 %
    Favored  : 79.62 %
  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:  2.67 (0.22), residues: 1302
  helix:  1.98 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -3.79 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  27 
 PHE   0.016   0.003   PHE A 185 
 TRP   0.010   0.001   TRP E 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10368)
  covalent geometry    : angle       0.59265 (14028)
  hydrogen bonds       : bond        0.03609 ( 1045)
  hydrogen bonds       : angle       3.51018 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.8789 (m) cc_final: 0.8355 (p)
REVERT: A  110 ASN cc_start: 0.8663 (m110) cc_final: 0.8049 (t0)
REVERT: A  121 LYS cc_start: 0.9424 (mttt) cc_final: 0.9174 (mtpp)
REVERT: A  142 ASP cc_start: 0.8336 (t0) cc_final: 0.8097 (t0)
REVERT: A  178 LYS cc_start: 0.9292 (mttm) cc_final: 0.8890 (tppp)
REVERT: A  183 ILE cc_start: 0.9003 (mt) cc_final: 0.8743 (tp)
REVERT: B  142 ASP cc_start: 0.7856 (t0) cc_final: 0.7562 (t0)
REVERT: B  164 GLN cc_start: 0.8482 (tt0) cc_final: 0.8179 (tt0)
REVERT: C   99 LEU cc_start: 0.9153 (mm) cc_final: 0.8932 (mm)
REVERT: C  110 ASN cc_start: 0.8814 (m110) cc_final: 0.8011 (t0)
REVERT: C  121 LYS cc_start: 0.9393 (mttt) cc_final: 0.9140 (mtpt)
REVERT: C  142 ASP cc_start: 0.8121 (t0) cc_final: 0.7848 (t0)
REVERT: C  164 GLN cc_start: 0.8362 (tt0) cc_final: 0.8154 (tp-100)
REVERT: D   58 SER cc_start: 0.8620 (m) cc_final: 0.8135 (p)
REVERT: D  121 LYS cc_start: 0.9409 (mttt) cc_final: 0.9148 (mtpp)
REVERT: D  183 ILE cc_start: 0.8958 (mt) cc_final: 0.8731 (tp)
REVERT: D  188 MET cc_start: 0.9176 (mtp) cc_final: 0.8960 (mtp)
REVERT: E  110 ASN cc_start: 0.8625 (m110) cc_final: 0.8091 (t0)
REVERT: E  142 ASP cc_start: 0.7853 (t0) cc_final: 0.7583 (t0)
REVERT: E  152 LEU cc_start: 0.9349 (pp) cc_final: 0.8962 (tp)
REVERT: F  110 ASN cc_start: 0.8782 (m110) cc_final: 0.7988 (t0)
REVERT: F  121 LYS cc_start: 0.9437 (mttt) cc_final: 0.9161 (mtpt)
  outliers start: 42
  outliers final: 25
  residues processed: 248
  average time/residue: 0.0785
  time to fit residues: 28.3147
Evaluate side-chains
  238 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue  107 VAL
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 92 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.100236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.076969 restraints weight = 25602.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.080101 restraints weight = 16824.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.082314 restraints weight = 12767.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.083823 restraints weight = 10516.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.084963 restraints weight = 9166.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10368  Z= 0.131
  Angle     :  0.571  11.178  14028  Z= 0.296
  Chirality :  0.037   0.366   1662
  Planarity :  0.004   0.028   1884
  Dihedral  :  3.429  12.809   1458
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.48 %
    Favored  : 80.19 %
  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:  2.95 (0.22), residues: 1302
  helix:  2.19 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.96 (0.62), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  15 
 PHE   0.017   0.002   PHE F 185 
 TRP   0.010   0.001   TRP E 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10368)
  covalent geometry    : angle       0.57108 (14028)
  hydrogen bonds       : bond        0.03342 ( 1045)
  hydrogen bonds       : angle       3.37111 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 232
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8253 (mm-30)
REVERT: A   58 SER cc_start: 0.8695 (m) cc_final: 0.8299 (p)
REVERT: A  110 ASN cc_start: 0.8669 (m110) cc_final: 0.7954 (t0)
REVERT: A  121 LYS cc_start: 0.9452 (mttt) cc_final: 0.9190 (mtpp)
REVERT: A  142 ASP cc_start: 0.8264 (t0) cc_final: 0.7907 (t0)
REVERT: A  178 LYS cc_start: 0.9274 (mttm) cc_final: 0.8887 (tppp)
REVERT: A  183 ILE cc_start: 0.8960 (mt) cc_final: 0.8701 (tp)
REVERT: A  188 MET cc_start: 0.9062 (mtp) cc_final: 0.8746 (mtp)
REVERT: B  142 ASP cc_start: 0.7838 (t0) cc_final: 0.7472 (t0)
REVERT: B  164 GLN cc_start: 0.8417 (tt0) cc_final: 0.8091 (tt0)
REVERT: C   79 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: C  110 ASN cc_start: 0.8785 (m110) cc_final: 0.8060 (t0)
REVERT: C  121 LYS cc_start: 0.9404 (mttt) cc_final: 0.9155 (mtpt)
REVERT: C  142 ASP cc_start: 0.8055 (t0) cc_final: 0.7822 (t0)
REVERT: D   58 SER cc_start: 0.8730 (m) cc_final: 0.8232 (p)
REVERT: D  121 LYS cc_start: 0.9438 (mttt) cc_final: 0.9195 (mtpp)
REVERT: D  188 MET cc_start: 0.9176 (mtp) cc_final: 0.8914 (mtp)
REVERT: E  110 ASN cc_start: 0.8502 (m110) cc_final: 0.8035 (t0)
REVERT: E  142 ASP cc_start: 0.7920 (t0) cc_final: 0.7540 (t0)
REVERT: E  152 LEU cc_start: 0.9360 (pp) cc_final: 0.9000 (tp)
REVERT: E  178 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8927 (tppp)
REVERT: F  110 ASN cc_start: 0.8747 (m110) cc_final: 0.7899 (t0)
REVERT: F  121 LYS cc_start: 0.9452 (mttt) cc_final: 0.9185 (mtpt)
  outliers start: 35
  outliers final: 21
  residues processed: 252
  average time/residue: 0.0739
  time to fit residues: 27.4781
Evaluate side-chains
  233 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  181 LYS
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 118 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 116 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
C 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.101321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.077987 restraints weight = 25253.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.081247 restraints weight = 16274.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.083617 restraints weight = 12209.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.085189 restraints weight = 9939.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.086384 restraints weight = 8610.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
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   0.039  10368  Z= 0.130
  Angle     :  0.619  11.669  14028  Z= 0.306
  Chirality :  0.038   0.392   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.420  13.138   1458
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.00 %
    Favored  : 78.86 %
  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:  2.99 (0.22), residues: 1302
  helix:  2.20 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.27 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  15 
 PHE   0.021   0.003   PHE F 185 
 TRP   0.010   0.001   TRP E 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10368)
  covalent geometry    : angle       0.61883 (14028)
  hydrogen bonds       : bond        0.03321 ( 1045)
  hydrogen bonds       : angle       3.40828 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 233
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8480 (mm-30)
REVERT: A   58 SER cc_start: 0.8968 (m) cc_final: 0.8562 (p)
REVERT: A  121 LYS cc_start: 0.9393 (mttt) cc_final: 0.9117 (mtpp)
REVERT: A  142 ASP cc_start: 0.8183 (t0) cc_final: 0.7757 (t0)
REVERT: A  178 LYS cc_start: 0.9298 (mttm) cc_final: 0.8916 (tppp)
REVERT: A  183 ILE cc_start: 0.9030 (mt) cc_final: 0.8757 (tp)
REVERT: A  188 MET cc_start: 0.9059 (mtp) cc_final: 0.8791 (mtp)
REVERT: A  196 ILE cc_start: 0.9000 (tp) cc_final: 0.8713 (tp)
REVERT: B  142 ASP cc_start: 0.7951 (t0) cc_final: 0.7485 (t0)
REVERT: B  164 GLN cc_start: 0.8496 (tt0) cc_final: 0.8116 (tt0)
REVERT: C   79 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7805 (tm-30)
REVERT: C  110 ASN cc_start: 0.8806 (m110) cc_final: 0.8043 (t0)
REVERT: C  121 LYS cc_start: 0.9345 (mttt) cc_final: 0.9083 (mtpt)
REVERT: C  142 ASP cc_start: 0.8111 (t0) cc_final: 0.7784 (t0)
REVERT: D   58 SER cc_start: 0.8960 (m) cc_final: 0.8493 (p)
REVERT: D  121 LYS cc_start: 0.9386 (mttt) cc_final: 0.9145 (mtpp)
REVERT: D  188 MET cc_start: 0.9181 (mtp) cc_final: 0.8892 (mtp)
REVERT: D  215 LEU cc_start: 0.8853 (tt) cc_final: 0.8639 (pp)
REVERT: E   95 GLU cc_start: 0.8414 (tp30) cc_final: 0.8114 (tp30)
REVERT: E  110 ASN cc_start: 0.8520 (m110) cc_final: 0.7944 (t0)
REVERT: E  142 ASP cc_start: 0.7949 (t0) cc_final: 0.7472 (t0)
REVERT: E  152 LEU cc_start: 0.9346 (pp) cc_final: 0.8876 (tp)
REVERT: F  110 ASN cc_start: 0.8817 (m110) cc_final: 0.7869 (t0)
REVERT: F  121 LYS cc_start: 0.9392 (mttt) cc_final: 0.9108 (mtpt)
REVERT: F  144 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (pm20)
  outliers start: 33
  outliers final: 24
  residues processed: 254
  average time/residue: 0.0845
  time to fit residues: 30.2381
Evaluate side-chains
  229 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  181 LYS
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  144 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 120 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0060
   chunk 66 optimal weight:    0.8980
   chunk 108 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
D 220 GLN
E 220 GLN
F 164 GLN
F 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.079460 restraints weight = 25563.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.082733 restraints weight = 16648.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.085038 restraints weight = 12554.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.086565 restraints weight = 10256.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.087733 restraints weight = 8905.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10368  Z= 0.127
  Angle     :  0.665  12.322  14028  Z= 0.321
  Chirality :  0.040   0.396   1662
  Planarity :  0.004   0.025   1884
  Dihedral  :  3.464  14.105   1458
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.00 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.04 (0.22), residues: 1302
  helix:  2.23 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.22 (0.69), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 139 
 PHE   0.022   0.002   PHE F 185 
 TRP   0.011   0.001   TRP F 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10368)
  covalent geometry    : angle       0.66467 (14028)
  hydrogen bonds       : bond        0.03222 ( 1045)
  hydrogen bonds       : angle       3.41520 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 224
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: A   58 SER cc_start: 0.8946 (m) cc_final: 0.8533 (p)
REVERT: A  142 ASP cc_start: 0.8104 (t0) cc_final: 0.7715 (t0)
REVERT: A  178 LYS cc_start: 0.9278 (mttm) cc_final: 0.8902 (tppp)
REVERT: A  183 ILE cc_start: 0.9016 (mt) cc_final: 0.8763 (tp)
REVERT: A  188 MET cc_start: 0.9026 (mtp) cc_final: 0.8770 (mtp)
REVERT: A  196 ILE cc_start: 0.8967 (tp) cc_final: 0.8671 (tp)
REVERT: B  142 ASP cc_start: 0.7829 (t0) cc_final: 0.7442 (t0)
REVERT: B  164 GLN cc_start: 0.8414 (tt0) cc_final: 0.8086 (tt0)
REVERT: C   79 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: C  110 ASN cc_start: 0.8766 (m110) cc_final: 0.7906 (t0)
REVERT: C  142 ASP cc_start: 0.7938 (t0) cc_final: 0.7673 (t0)
REVERT: D   58 SER cc_start: 0.8941 (m) cc_final: 0.8463 (p)
REVERT: D  188 MET cc_start: 0.9147 (mtp) cc_final: 0.8847 (mtp)
REVERT: E  142 ASP cc_start: 0.8107 (t0) cc_final: 0.7719 (t70)
REVERT: E  152 LEU cc_start: 0.9314 (pp) cc_final: 0.8874 (tp)
REVERT: F  110 ASN cc_start: 0.8797 (m110) cc_final: 0.7876 (t0)
REVERT: F  118 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8014 (mt-10)
REVERT: F  185 PHE cc_start: 0.8489 (t80) cc_final: 0.8133 (t80)
REVERT: F  204 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8251 (ttm)
  outliers start: 37
  outliers final: 18
  residues processed: 247
  average time/residue: 0.0734
  time to fit residues: 26.2893
Evaluate side-chains
  218 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  181 LYS
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 74 optimal weight:    0.8980
   chunk 114 optimal weight:    0.7980
   chunk 1 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
C 220 GLN
D 166 ASN
E 166 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.103162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.079886 restraints weight = 25315.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.083265 restraints weight = 16464.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.085628 restraints weight = 12371.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.087289 restraints weight = 10086.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.088477 restraints weight = 8688.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10368  Z= 0.134
  Angle     :  0.678  12.544  14028  Z= 0.333
  Chirality :  0.041   0.395   1662
  Planarity :  0.003   0.024   1884
  Dihedral  :  3.452  13.535   1458
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.95 %
    Favored  : 76.95 %
  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:  2.94 (0.23), residues: 1302
  helix:  2.16 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.19 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  15 
 PHE   0.020   0.003   PHE F 185 
 TRP   0.012   0.001   TRP C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10368)
  covalent geometry    : angle       0.67795 (14028)
  hydrogen bonds       : bond        0.03358 ( 1045)
  hydrogen bonds       : angle       3.38170 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 217
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8287 (mm-30)
REVERT: A   58 SER cc_start: 0.8800 (m) cc_final: 0.8378 (p)
REVERT: A  142 ASP cc_start: 0.7997 (t0) cc_final: 0.7712 (t0)
REVERT: A  183 ILE cc_start: 0.9011 (mt) cc_final: 0.8762 (tp)
REVERT: A  188 MET cc_start: 0.9026 (mtp) cc_final: 0.8798 (mtp)
REVERT: A  196 ILE cc_start: 0.8932 (tp) cc_final: 0.8633 (tp)
REVERT: B  142 ASP cc_start: 0.7730 (t0) cc_final: 0.7420 (t0)
REVERT: B  164 GLN cc_start: 0.8432 (tt0) cc_final: 0.8078 (tt0)
REVERT: C   79 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: C  110 ASN cc_start: 0.8795 (m110) cc_final: 0.7944 (t0)
REVERT: D   58 SER cc_start: 0.8876 (m) cc_final: 0.8414 (p)
REVERT: D  188 MET cc_start: 0.9142 (mtp) cc_final: 0.8850 (mtp)
REVERT: E  142 ASP cc_start: 0.8044 (t0) cc_final: 0.7705 (t70)
REVERT: E  152 LEU cc_start: 0.9323 (pp) cc_final: 0.8902 (tp)
REVERT: F  110 ASN cc_start: 0.8768 (m110) cc_final: 0.7955 (t0)
REVERT: F  204 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8206 (ttm)
  outliers start: 22
  outliers final: 16
  residues processed: 227
  average time/residue: 0.0762
  time to fit residues: 25.2062
Evaluate side-chains
  224 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  181 LYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 220 GLN
B 166 ASN
C 166 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.079575 restraints weight = 25478.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.082846 restraints weight = 16628.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.085137 restraints weight = 12539.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.086668 restraints weight = 10276.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.087828 restraints weight = 8943.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  10368  Z= 0.139
  Angle     :  0.673  12.488  14028  Z= 0.335
  Chirality :  0.041   0.404   1662
  Planarity :  0.003   0.024   1884
  Dihedral  :  3.449  13.985   1458
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.90 %
    Favored  : 76.29 %
  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:  2.90 (0.22), residues: 1302
  helix:  2.14 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.21 (0.65), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  15 
 PHE   0.021   0.002   PHE F 185 
 TRP   0.012   0.001   TRP C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10368)
  covalent geometry    : angle       0.67298 (14028)
  hydrogen bonds       : bond        0.03391 ( 1045)
  hydrogen bonds       : angle       3.43116 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: A   58 SER cc_start: 0.8819 (m) cc_final: 0.8382 (p)
REVERT: A  142 ASP cc_start: 0.8084 (t0) cc_final: 0.7785 (t0)
REVERT: A  183 ILE cc_start: 0.9039 (mt) cc_final: 0.8760 (tp)
REVERT: A  188 MET cc_start: 0.9069 (mtp) cc_final: 0.8840 (mtp)
REVERT: A  196 ILE cc_start: 0.8927 (tp) cc_final: 0.8643 (tp)
REVERT: A  220 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7729 (tm-30)
REVERT: B  142 ASP cc_start: 0.7734 (t0) cc_final: 0.7418 (t0)
REVERT: B  164 GLN cc_start: 0.8468 (tt0) cc_final: 0.8110 (tt0)
REVERT: C   79 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: C  128 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8750 (mt-10)
REVERT: D   58 SER cc_start: 0.8900 (m) cc_final: 0.8443 (p)
REVERT: D  188 MET cc_start: 0.9160 (mtp) cc_final: 0.8863 (mtp)
REVERT: E  142 ASP cc_start: 0.8041 (t0) cc_final: 0.7675 (t70)
REVERT: E  152 LEU cc_start: 0.9356 (pp) cc_final: 0.8896 (tp)
REVERT: F  110 ASN cc_start: 0.8749 (m110) cc_final: 0.7951 (t0)
REVERT: F  204 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8206 (ttm)
  outliers start: 19
  outliers final: 16
  residues processed: 219
  average time/residue: 0.0746
  time to fit residues: 24.0946
Evaluate side-chains
  217 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 107 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
B 220 GLN
C 220 GLN
E 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.102888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.079642 restraints weight = 25362.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.082966 restraints weight = 16713.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.085271 restraints weight = 12630.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.086868 restraints weight = 10328.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.087597 restraints weight = 8968.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  10368  Z= 0.139
  Angle     :  0.681  13.461  14028  Z= 0.341
  Chirality :  0.041   0.404   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.465  14.138   1458
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 22.38 %
    Favored  : 75.62 %
  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:  2.93 (0.22), residues: 1302
  helix:  2.16 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.22 (0.65), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 PHE   0.021   0.003   PHE F 185 
 TRP   0.014   0.001   TRP C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10368)
  covalent geometry    : angle       0.68138 (14028)
  hydrogen bonds       : bond        0.03410 ( 1045)
  hydrogen bonds       : angle       3.45009 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8264 (mm-30)
REVERT: A   58 SER cc_start: 0.8841 (m) cc_final: 0.8402 (p)
REVERT: A  142 ASP cc_start: 0.8173 (t0) cc_final: 0.7812 (t0)
REVERT: A  183 ILE cc_start: 0.9007 (mt) cc_final: 0.8767 (tp)
REVERT: A  188 MET cc_start: 0.9063 (mtp) cc_final: 0.8843 (mtp)
REVERT: A  196 ILE cc_start: 0.8909 (tp) cc_final: 0.8624 (tp)
REVERT: B  142 ASP cc_start: 0.7749 (t0) cc_final: 0.7423 (t0)
REVERT: B  164 GLN cc_start: 0.8541 (tt0) cc_final: 0.8150 (tt0)
REVERT: C   79 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: D   58 SER cc_start: 0.8908 (m) cc_final: 0.8458 (p)
REVERT: E  142 ASP cc_start: 0.8040 (t0) cc_final: 0.7671 (t70)
REVERT: E  152 LEU cc_start: 0.9352 (pp) cc_final: 0.8892 (tp)
REVERT: F  110 ASN cc_start: 0.8726 (m110) cc_final: 0.7905 (t0)
REVERT: F  204 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (ttm)
  outliers start: 21
  outliers final: 16
  residues processed: 221
  average time/residue: 0.0737
  time to fit residues: 23.5554
Evaluate side-chains
  216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.1184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.103155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.079453 restraints weight = 25395.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.082883 restraints weight = 16537.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.085190 restraints weight = 12444.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.086791 restraints weight = 10189.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.087868 restraints weight = 8823.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10368  Z= 0.144
  Angle     :  0.694  13.686  14028  Z= 0.349
  Chirality :  0.041   0.407   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.463  14.369   1458
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.76 %
    Favored  : 75.62 %
  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:  2.89 (0.22), residues: 1302
  helix:  2.13 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.25 (0.65), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 221 
 PHE   0.021   0.002   PHE F 185 
 TRP   0.010   0.001   TRP B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10368)
  covalent geometry    : angle       0.69429 (14028)
  hydrogen bonds       : bond        0.03412 ( 1045)
  hydrogen bonds       : angle       3.43070 ( 3135)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8388 (mm-30)
REVERT: A   58 SER cc_start: 0.8932 (m) cc_final: 0.8500 (p)
REVERT: A  142 ASP cc_start: 0.8159 (t0) cc_final: 0.7728 (t0)
REVERT: A  183 ILE cc_start: 0.9038 (mt) cc_final: 0.8805 (tp)
REVERT: A  188 MET cc_start: 0.9060 (mtp) cc_final: 0.8817 (mtp)
REVERT: A  196 ILE cc_start: 0.8912 (tp) cc_final: 0.8639 (tp)
REVERT: B  142 ASP cc_start: 0.7804 (t0) cc_final: 0.7422 (t0)
REVERT: B  164 GLN cc_start: 0.8591 (tt0) cc_final: 0.8149 (tt0)
REVERT: C   79 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7842 (tm-30)
REVERT: C  110 ASN cc_start: 0.8708 (m-40) cc_final: 0.7792 (t0)
REVERT: C  181 LYS cc_start: 0.9287 (mttt) cc_final: 0.9047 (ttmt)
REVERT: C  204 MET cc_start: 0.8732 (ttt) cc_final: 0.8317 (ptm)
REVERT: D   58 SER cc_start: 0.9009 (m) cc_final: 0.8567 (p)
REVERT: D  188 MET cc_start: 0.9055 (mtp) cc_final: 0.8728 (mtp)
REVERT: E  142 ASP cc_start: 0.8090 (t0) cc_final: 0.7675 (t70)
REVERT: E  152 LEU cc_start: 0.9341 (pp) cc_final: 0.8873 (tp)
REVERT: E  181 LYS cc_start: 0.9511 (mmtp) cc_final: 0.8977 (mmtt)
REVERT: F  110 ASN cc_start: 0.8761 (m110) cc_final: 0.7880 (t0)
REVERT: F  204 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (ttm)
  outliers start: 17
  outliers final: 15
  residues processed: 214
  average time/residue: 0.0808
  time to fit residues: 25.2329
Evaluate side-chains
  218 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0670
   chunk 113 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
D 166 ASN
E 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.104082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.080601 restraints weight = 25324.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.083962 restraints weight = 16542.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.086313 restraints weight = 12480.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.087994 restraints weight = 10193.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.089136 restraints weight = 8795.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10368  Z= 0.138
  Angle     :  0.699  14.154  14028  Z= 0.349
  Chirality :  0.041   0.406   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.477  14.372   1458
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 23.14 %
    Favored  : 75.33 %
  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:  2.89 (0.22), residues: 1302
  helix:  2.15 (0.14), residues: 1260
  sheet:  None (None), residues: 0
  loop : -5.88 (0.21), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  27 
 PHE   0.021   0.003   PHE F 185 
 TRP   0.011   0.001   TRP B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10368)
  covalent geometry    : angle       0.69878 (14028)
  hydrogen bonds       : bond        0.03309 ( 1045)
  hydrogen bonds       : angle       3.41101 ( 3135)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.12 seconds
wall clock time: 23 minutes 10.01 seconds (1390.01 seconds total)