Starting phenix.real_space_refine
on Fri Jan 17 00:15:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6r_28889/01_2025/8f6r_28889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6r_28889/01_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6r_28889/01_2025/8f6r_28889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6r_28889/01_2025/8f6r_28889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6r_28889/01_2025/8f6r_28889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6r_28889/01_2025/8f6r_28889.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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:
    C, B, E, D, F
  Time building chain proxies: 4.72, per 1000 atoms: 0.46
  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: 3.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.94
  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: 3.67

  Time building geometry restraints manager: 3.71 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             2.330
  Set stop_for_unknowns flag:              0.020
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.990
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.040
-------------------------------------------------------------------------------
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= 0.331
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (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
 TRP   0.010   0.002   TRP C  52 
 PHE   0.002   0.000   PHE B 185 
 ARG   0.002   0.000   ARG F  76 

*********************** 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  : 1.160 
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: 0.2480
  time to fit residues: 121.0706
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  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.100543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.077949 restraints weight = 24906.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.081372 restraints weight = 15476.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.083710 restraints weight = 11378.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10368  Z= 0.232
  Angle     :  0.609   9.680  14028  Z= 0.319
  Chirality :  0.040   0.345   1662
  Planarity :  0.005   0.034   1884
  Dihedral  :  3.452  13.250   1458
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.95 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.21), residues: 1302
  helix:  1.69 (0.13), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.75 (0.60), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 201 
 PHE   0.025   0.002   PHE A 185 
 ARG   0.004   0.000   ARG C 165 

*********************** 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
  307 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 278
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ASN cc_start: 0.8621 (m110) cc_final: 0.8051 (t0)
REVERT: A  121 LYS cc_start: 0.9396 (mttt) cc_final: 0.9108 (mtpp)
REVERT: A  142 ASP cc_start: 0.8284 (t0) cc_final: 0.7931 (t0)
REVERT: A  152 LEU cc_start: 0.9338 (pp) cc_final: 0.8879 (tp)
REVERT: A  190 LEU cc_start: 0.9272 (mt) cc_final: 0.8967 (mt)
REVERT: B  118 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7909 (mt-10)
REVERT: B  121 LYS cc_start: 0.9400 (mttt) cc_final: 0.9189 (mtpp)
REVERT: B  142 ASP cc_start: 0.7923 (t0) cc_final: 0.7635 (t0)
REVERT: B  164 GLN cc_start: 0.8419 (tt0) cc_final: 0.8143 (tt0)
REVERT: C  110 ASN cc_start: 0.8707 (m110) cc_final: 0.8015 (t0)
REVERT: C  121 LYS cc_start: 0.9372 (mttt) cc_final: 0.9098 (mtpt)
REVERT: C  142 ASP cc_start: 0.8179 (t0) cc_final: 0.7930 (t0)
REVERT: D   58 SER cc_start: 0.8713 (m) cc_final: 0.8312 (p)
REVERT: D  110 ASN cc_start: 0.8488 (m110) cc_final: 0.7884 (t0)
REVERT: D  121 LYS cc_start: 0.9397 (mttt) cc_final: 0.9114 (mtpp)
REVERT: D  152 LEU cc_start: 0.9296 (pp) cc_final: 0.8896 (tp)
REVERT: E  110 ASN cc_start: 0.8619 (m110) cc_final: 0.8079 (t0)
REVERT: E  142 ASP cc_start: 0.7996 (t0) cc_final: 0.7697 (t0)
REVERT: E  152 LEU cc_start: 0.9322 (pp) cc_final: 0.8850 (tp)
REVERT: E  164 GLN cc_start: 0.8459 (tt0) cc_final: 0.8258 (tt0)
REVERT: F  110 ASN cc_start: 0.8698 (m110) cc_final: 0.8059 (t0)
REVERT: F  121 LYS cc_start: 0.9395 (mttt) cc_final: 0.9088 (mtpt)
REVERT: F  142 ASP cc_start: 0.7811 (t0) cc_final: 0.7558 (t0)
REVERT: F  185 PHE cc_start: 0.8706 (t80) cc_final: 0.8215 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 293
  average time/residue: 0.2119
  time to fit residues: 87.8659
Evaluate side-chains
  238 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
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 62 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.100890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.078120 restraints weight = 25290.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.081274 restraints weight = 16397.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.083512 restraints weight = 12341.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10368  Z= 0.201
  Angle     :  0.587  10.276  14028  Z= 0.305
  Chirality :  0.039   0.382   1662
  Planarity :  0.004   0.032   1884
  Dihedral  :  3.428  12.882   1458
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.22), residues: 1302
  helix:  2.17 (0.14), residues: 1242
  sheet:  None (None), residues: 0
  loop : -3.94 (0.58), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 201 
 PHE   0.018   0.003   PHE A 185 
 ARG   0.004   0.000   ARG E  27 

*********************** 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
  268 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 1.154 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8206 (mm-30)
REVERT: A   58 SER cc_start: 0.8729 (m) cc_final: 0.8294 (p)
REVERT: A  110 ASN cc_start: 0.8623 (m110) cc_final: 0.7936 (t0)
REVERT: A  121 LYS cc_start: 0.9427 (mttt) cc_final: 0.9140 (mtpp)
REVERT: A  142 ASP cc_start: 0.8311 (t0) cc_final: 0.8075 (t0)
REVERT: A  178 LYS cc_start: 0.9272 (mttm) cc_final: 0.8906 (tppp)
REVERT: B  142 ASP cc_start: 0.7850 (t0) cc_final: 0.7565 (t0)
REVERT: B  164 GLN cc_start: 0.8515 (tt0) cc_final: 0.8202 (tp40)
REVERT: C  110 ASN cc_start: 0.8803 (m110) cc_final: 0.7988 (t0)
REVERT: C  121 LYS cc_start: 0.9385 (mttt) cc_final: 0.9169 (mtpt)
REVERT: C  142 ASP cc_start: 0.8027 (t0) cc_final: 0.7795 (t0)
REVERT: C  152 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8910 (tt)
REVERT: D   58 SER cc_start: 0.8696 (m) cc_final: 0.8219 (p)
REVERT: D  121 LYS cc_start: 0.9418 (mttt) cc_final: 0.9161 (mtpp)
REVERT: D  188 MET cc_start: 0.9141 (mtp) cc_final: 0.8874 (mtp)
REVERT: E  110 ASN cc_start: 0.8587 (m110) cc_final: 0.8041 (t0)
REVERT: E  142 ASP cc_start: 0.7842 (t0) cc_final: 0.7583 (t0)
REVERT: E  164 GLN cc_start: 0.8502 (tt0) cc_final: 0.8267 (tt0)
REVERT: E  183 ILE cc_start: 0.9110 (mt) cc_final: 0.8748 (tp)
REVERT: F  110 ASN cc_start: 0.8696 (m110) cc_final: 0.7984 (t0)
REVERT: F  118 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7892 (mt-10)
REVERT: F  121 LYS cc_start: 0.9438 (mttt) cc_final: 0.9178 (mtpt)
REVERT: F  142 ASP cc_start: 0.7857 (t0) cc_final: 0.7570 (t0)
REVERT: F  185 PHE cc_start: 0.8680 (t80) cc_final: 0.8150 (t80)
  outliers start: 31
  outliers final: 18
  residues processed: 252
  average time/residue: 0.2057
  time to fit residues: 74.0560
Evaluate side-chains
  232 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 213
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
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   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
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  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  190 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0060
   chunk 73 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7598

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.078623 restraints weight = 25224.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.081840 restraints weight = 16469.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.084084 restraints weight = 12414.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10368  Z= 0.192
  Angle     :  0.584  11.420  14028  Z= 0.299
  Chirality :  0.037   0.374   1662
  Planarity :  0.004   0.029   1884
  Dihedral  :  3.434  13.285   1458
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.05 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.04 (0.22), residues: 1302
  helix:  2.24 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.93 (0.66), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 201 
 PHE   0.007   0.001   PHE A 185 
 ARG   0.003   0.000   ARG C  27 

*********************** 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
  279 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 245
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8276 (mm-30)
REVERT: A   58 SER cc_start: 0.8739 (m) cc_final: 0.8283 (p)
REVERT: A  121 LYS cc_start: 0.9439 (mttt) cc_final: 0.9161 (mtpp)
REVERT: A  142 ASP cc_start: 0.8265 (t0) cc_final: 0.7952 (t0)
REVERT: A  178 LYS cc_start: 0.9299 (mttm) cc_final: 0.8941 (tppp)
REVERT: A  196 ILE cc_start: 0.9010 (tp) cc_final: 0.8724 (tp)
REVERT: B  142 ASP cc_start: 0.7837 (t0) cc_final: 0.7336 (t0)
REVERT: B  164 GLN cc_start: 0.8419 (tt0) cc_final: 0.8129 (tt0)
REVERT: C   12 GLU cc_start: 0.8576 (tp30) cc_final: 0.8361 (tp30)
REVERT: C   79 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: C  110 ASN cc_start: 0.8769 (m110) cc_final: 0.8000 (t0)
REVERT: C  121 LYS cc_start: 0.9391 (mttt) cc_final: 0.9156 (mtpp)
REVERT: C  142 ASP cc_start: 0.8148 (t0) cc_final: 0.7863 (t0)
REVERT: D   58 SER cc_start: 0.8835 (m) cc_final: 0.8365 (p)
REVERT: D  121 LYS cc_start: 0.9436 (mttt) cc_final: 0.9192 (mtpp)
REVERT: D  152 LEU cc_start: 0.9331 (pp) cc_final: 0.8946 (tt)
REVERT: D  188 MET cc_start: 0.9172 (mtp) cc_final: 0.8868 (mtp)
REVERT: E  142 ASP cc_start: 0.7931 (t0) cc_final: 0.7528 (t0)
REVERT: F  110 ASN cc_start: 0.8846 (m110) cc_final: 0.7918 (t0)
REVERT: F  121 LYS cc_start: 0.9457 (mttt) cc_final: 0.9207 (mtpt)
REVERT: F  142 ASP cc_start: 0.7604 (t0) cc_final: 0.7328 (t0)
REVERT: F  185 PHE cc_start: 0.8626 (t80) cc_final: 0.8123 (t80)
  outliers start: 34
  outliers final: 18
  residues processed: 269
  average time/residue: 0.2130
  time to fit residues: 82.2707
Evaluate side-chains
  242 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 224
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
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   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   53 LEU
Chi-restraints excluded: chain D residue  190 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 120 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
B 220 GLN
C 220 GLN
D 220 GLN
F 164 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.102054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.078260 restraints weight = 25313.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.081565 restraints weight = 16614.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.083838 restraints weight = 12602.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10368  Z= 0.204
  Angle     :  0.640  13.272  14028  Z= 0.316
  Chirality :  0.040   0.396   1662
  Planarity :  0.003   0.027   1884
  Dihedral  :  3.436  13.573   1458
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.19 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.22), residues: 1302
  helix:  2.21 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.99 (0.64), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 201 
 PHE   0.016   0.002   PHE C 185 
 ARG   0.003   0.000   ARG C  15 

*********************** 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
  263 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 235
  time to evaluate  : 1.330 
Fit side-chains
REVERT: A   16 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8456 (mm-30)
REVERT: A   58 SER cc_start: 0.8997 (m) cc_final: 0.8588 (p)
REVERT: A   95 GLU cc_start: 0.8415 (tp30) cc_final: 0.8087 (tp30)
REVERT: A  121 LYS cc_start: 0.9398 (mttt) cc_final: 0.9166 (mtpp)
REVERT: A  142 ASP cc_start: 0.8200 (t0) cc_final: 0.7746 (t0)
REVERT: A  178 LYS cc_start: 0.9305 (mttm) cc_final: 0.8874 (tppp)
REVERT: A  188 MET cc_start: 0.8978 (mtp) cc_final: 0.8599 (mtp)
REVERT: A  196 ILE cc_start: 0.8997 (tp) cc_final: 0.8706 (tp)
REVERT: B  142 ASP cc_start: 0.7964 (t0) cc_final: 0.7480 (t0)
REVERT: C   79 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7845 (tm-30)
REVERT: C  110 ASN cc_start: 0.8782 (m110) cc_final: 0.8005 (t0)
REVERT: C  121 LYS cc_start: 0.9365 (mttt) cc_final: 0.9134 (mtpt)
REVERT: C  142 ASP cc_start: 0.8099 (t0) cc_final: 0.7685 (t0)
REVERT: D   58 SER cc_start: 0.8966 (m) cc_final: 0.8502 (p)
REVERT: D  121 LYS cc_start: 0.9401 (mttt) cc_final: 0.9164 (mtpp)
REVERT: D  152 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8922 (tt)
REVERT: D  188 MET cc_start: 0.9189 (mtp) cc_final: 0.8856 (mtp)
REVERT: E  142 ASP cc_start: 0.8058 (t0) cc_final: 0.7536 (t0)
REVERT: E  181 LYS cc_start: 0.9504 (mmtp) cc_final: 0.9022 (mmtt)
REVERT: E  196 ILE cc_start: 0.8640 (tp) cc_final: 0.8433 (tp)
REVERT: F  110 ASN cc_start: 0.8804 (m110) cc_final: 0.7840 (t0)
REVERT: F  121 LYS cc_start: 0.9400 (mttt) cc_final: 0.9131 (mtpt)
REVERT: F  142 ASP cc_start: 0.7520 (t0) cc_final: 0.7214 (t0)
REVERT: F  204 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8309 (ttm)
  outliers start: 28
  outliers final: 18
  residues processed: 249
  average time/residue: 0.2038
  time to fit residues: 73.0828
Evaluate side-chains
  236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 216
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
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   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 D residue  152 LEU
Chi-restraints excluded: chain D residue  190 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 122 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.4984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.101233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.077496 restraints weight = 25452.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.080751 restraints weight = 16616.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.083067 restraints weight = 12534.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10368  Z= 0.232
  Angle     :  0.654  12.144  14028  Z= 0.326
  Chirality :  0.041   0.394   1662
  Planarity :  0.004   0.025   1884
  Dihedral  :  3.416  13.582   1458
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.38 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.22), residues: 1302
  helix:  2.07 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.26 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 201 
 PHE   0.021   0.003   PHE F 185 
 ARG   0.003   0.000   ARG B 139 

*********************** 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
  255 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 219
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8410 (mm-30)
REVERT: A   58 SER cc_start: 0.9031 (m) cc_final: 0.8634 (p)
REVERT: A  121 LYS cc_start: 0.9395 (mttt) cc_final: 0.9124 (mtpp)
REVERT: A  142 ASP cc_start: 0.8139 (t0) cc_final: 0.7758 (t0)
REVERT: A  178 LYS cc_start: 0.9295 (mttm) cc_final: 0.8925 (tppp)
REVERT: A  196 ILE cc_start: 0.9034 (tp) cc_final: 0.8742 (tp)
REVERT: B  118 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: B  142 ASP cc_start: 0.7924 (t0) cc_final: 0.7529 (t0)
REVERT: C   79 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: C  110 ASN cc_start: 0.8779 (m110) cc_final: 0.8029 (t0)
REVERT: C  142 ASP cc_start: 0.8014 (t0) cc_final: 0.7614 (t0)
REVERT: D   58 SER cc_start: 0.8968 (m) cc_final: 0.8502 (p)
REVERT: D  121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9148 (mtpp)
REVERT: D  188 MET cc_start: 0.9187 (mtp) cc_final: 0.8839 (mtp)
REVERT: E  142 ASP cc_start: 0.7997 (t0) cc_final: 0.7633 (t0)
REVERT: E  181 LYS cc_start: 0.9410 (mmtp) cc_final: 0.8957 (mmtt)
REVERT: F  110 ASN cc_start: 0.8814 (m110) cc_final: 0.7970 (t0)
REVERT: F  142 ASP cc_start: 0.7593 (t0) cc_final: 0.7276 (t0)
REVERT: F  204 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8352 (ttm)
  outliers start: 36
  outliers final: 21
  residues processed: 241
  average time/residue: 0.2106
  time to fit residues: 74.4366
Evaluate side-chains
  230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 208
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
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   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   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  190 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  144 GLU
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 125 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.102804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.079190 restraints weight = 25494.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082546 restraints weight = 16622.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.084930 restraints weight = 12501.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10368  Z= 0.208
  Angle     :  0.665  12.701  14028  Z= 0.331
  Chirality :  0.041   0.397   1662
  Planarity :  0.003   0.026   1884
  Dihedral  :  3.445  13.223   1458
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.22), residues: 1302
  helix:  2.11 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.20 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 201 
 PHE   0.021   0.003   PHE F 185 
 ARG   0.002   0.000   ARG B 139 

*********************** 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
  245 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: A   58 SER cc_start: 0.9018 (m) cc_final: 0.8615 (p)
REVERT: A  142 ASP cc_start: 0.8053 (t0) cc_final: 0.7698 (t0)
REVERT: A  178 LYS cc_start: 0.9278 (mttm) cc_final: 0.8909 (tppp)
REVERT: A  188 MET cc_start: 0.9020 (mtp) cc_final: 0.8687 (mtp)
REVERT: A  196 ILE cc_start: 0.8964 (tp) cc_final: 0.8666 (tp)
REVERT: B   95 GLU cc_start: 0.8370 (tp30) cc_final: 0.7953 (tp30)
REVERT: B   99 LEU cc_start: 0.8863 (mm) cc_final: 0.8490 (mm)
REVERT: B  118 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7867 (mm-30)
REVERT: B  142 ASP cc_start: 0.7917 (t0) cc_final: 0.7528 (t0)
REVERT: C   79 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: C  110 ASN cc_start: 0.8796 (m110) cc_final: 0.7942 (t0)
REVERT: C  142 ASP cc_start: 0.8008 (t0) cc_final: 0.7634 (t0)
REVERT: C  164 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8667 (tt0)
REVERT: D   58 SER cc_start: 0.8977 (m) cc_final: 0.8510 (p)
REVERT: D  121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9196 (mtpp)
REVERT: E  142 ASP cc_start: 0.8055 (t0) cc_final: 0.7674 (t0)
REVERT: E  181 LYS cc_start: 0.9416 (mmtp) cc_final: 0.8938 (mmtt)
REVERT: E  196 ILE cc_start: 0.8641 (tp) cc_final: 0.8438 (tp)
REVERT: F  110 ASN cc_start: 0.8826 (m110) cc_final: 0.7989 (t0)
REVERT: F  142 ASP cc_start: 0.7641 (t0) cc_final: 0.7291 (t0)
REVERT: F  204 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8305 (ttm)
  outliers start: 24
  outliers final: 19
  residues processed: 234
  average time/residue: 0.1945
  time to fit residues: 66.5415
Evaluate side-chains
  228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 208
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
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 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 D residue  180 ILE
Chi-restraints excluded: chain D residue  190 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  144 GLU
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6655 > 50:
  distance: 23 - 38:   5.407
  distance: 27 - 46:   6.056
  distance: 31 - 51:   4.324
  distance: 34 - 38:   3.847
  distance: 35 - 60:  12.547
  distance: 38 - 39:   3.902
  distance: 39 - 40:   5.158
  distance: 39 - 42:   8.598
  distance: 41 - 69:   6.955
  distance: 43 - 44:   7.569
  distance: 43 - 45:  13.470
  distance: 46 - 47:   4.801
  distance: 47 - 50:   6.344
  distance: 48 - 49:   6.557
  distance: 48 - 51:   3.161
  distance: 49 - 77:  22.927
  distance: 51 - 52:   8.232
  distance: 52 - 53:   7.036
  distance: 52 - 55:   3.970
  distance: 53 - 54:   4.062
  distance: 53 - 60:   7.840
  distance: 55 - 56:   6.225
  distance: 56 - 57:   4.101
  distance: 57 - 58:   4.277
  distance: 57 - 59:   5.931
  distance: 60 - 61:   8.201
  distance: 61 - 62:   5.051
  distance: 61 - 64:   8.966
  distance: 62 - 63:  11.453
  distance: 62 - 69:  13.600
  distance: 64 - 65:   5.310
  distance: 65 - 66:   4.219
  distance: 66 - 67:   5.567
  distance: 66 - 68:   4.184
  distance: 69 - 70:   9.255
  distance: 70 - 71:  15.117
  distance: 70 - 73:  12.181
  distance: 71 - 72:  29.464
  distance: 71 - 77:  27.697
  distance: 73 - 74:  11.898
  distance: 73 - 75:  14.632
  distance: 74 - 76:  11.167
  distance: 77 - 78:   9.257
  distance: 78 - 79:  23.995
  distance: 79 - 80:  22.284
  distance: 79 - 81:  26.824
  distance: 81 - 82:  21.816
  distance: 82 - 83:   6.937
  distance: 82 - 85:  14.609
  distance: 83 - 84:  10.786
  distance: 83 - 89:   9.564
  distance: 85 - 86:  14.344
  distance: 86 - 88:  15.818
  distance: 89 - 90:  11.723
  distance: 89 - 95:  10.819
  distance: 90 - 91:   8.836
  distance: 90 - 93:  11.589
  distance: 91 - 92:   7.573
  distance: 91 - 96:  14.345
  distance: 92 - 127:  13.487
  distance: 93 - 94:  19.125
  distance: 94 - 95:  13.318
  distance: 96 - 97:  14.008
  distance: 97 - 98:  17.012
  distance: 97 - 100:  16.710
  distance: 98 - 99:  13.188
  distance: 98 - 103:  14.132
  distance: 99 - 134:  31.028
  distance: 100 - 101:   3.640
  distance: 100 - 102:  23.597
  distance: 103 - 104:   6.772
  distance: 104 - 105:   3.837
  distance: 104 - 107:   4.579
  distance: 105 - 106:  15.247
  distance: 105 - 117:  16.830
  distance: 106 - 142:  20.864
  distance: 107 - 108:   8.608
  distance: 108 - 109:   5.322
  distance: 108 - 110:   7.306
  distance: 109 - 111:  10.594
  distance: 110 - 112:   8.339
  distance: 110 - 113:   5.701
  distance: 111 - 112:   4.821
  distance: 112 - 114:   6.475
  distance: 113 - 115:   7.642
  distance: 114 - 116:   4.142
  distance: 115 - 116:   8.483