Starting phenix.real_space_refine
on Thu Mar 13 19:56:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2025/7uxe_26858.cif"
  }
  resolution = 3.38
  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=   0.004 sd=   0.196
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      30      5.16       5
     C    6080      2.51       5
     N    1670      2.21       5
     O    1700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9480
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 948
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 3.14, per 1000 atoms: 0.33
  Number of scatterers: 9480
  At special positions: 0
  Unit cell: (118.75, 116.85, 59.85, 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      30     16.00
     O    1700      8.00
     N    1670      7.00
     C    6080      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: 2.43
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      67.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 50
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 69 through 82
    Processing helix  chain 'A' and resid 90 through 104
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 50
    Processing helix  chain 'B' and resid 58 through 67
    Processing helix  chain 'B' and resid 69 through 82
    Processing helix  chain 'B' and resid 90 through 104
    Processing helix  chain 'B' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG B 112 " --> pdb=" O   LYS B 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY C  39 " --> pdb=" O   LEU C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 58 through 67
    Processing helix  chain 'C' and resid 69 through 82
    Processing helix  chain 'C' and resid 90 through 104
    Processing helix  chain 'C' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG C 112 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY D  39 " --> pdb=" O   LEU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 58 through 67
    Processing helix  chain 'D' and resid 69 through 82
    Processing helix  chain 'D' and resid 90 through 104
    Processing helix  chain 'D' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY E  39 " --> pdb=" O   LEU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 50
    Processing helix  chain 'E' and resid 58 through 67
    Processing helix  chain 'E' and resid 69 through 82
    Processing helix  chain 'E' and resid 90 through 104
    Processing helix  chain 'E' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG E 112 " --> pdb=" O   LYS E 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY F  39 " --> pdb=" O   LEU F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 43 through 50
    Processing helix  chain 'F' and resid 58 through 67
    Processing helix  chain 'F' and resid 69 through 82
    Processing helix  chain 'F' and resid 90 through 104
    Processing helix  chain 'F' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG F 112 " --> pdb=" O   LYS F 108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY G  39 " --> pdb=" O   LEU G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 43 through 50
    Processing helix  chain 'G' and resid 58 through 67
    Processing helix  chain 'G' and resid 69 through 82
    Processing helix  chain 'G' and resid 90 through 104
    Processing helix  chain 'G' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG G 112 " --> pdb=" O   LYS G 108 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY H  39 " --> pdb=" O   LEU H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 43 through 50
    Processing helix  chain 'H' and resid 58 through 67
    Processing helix  chain 'H' and resid 69 through 82
    Processing helix  chain 'H' and resid 90 through 104
    Processing helix  chain 'H' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY I  39 " --> pdb=" O   LEU I  35 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 43 through 50
    Processing helix  chain 'I' and resid 58 through 67
    Processing helix  chain 'I' and resid 69 through 82
    Processing helix  chain 'I' and resid 90 through 104
    Processing helix  chain 'I' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG I 112 " --> pdb=" O   LYS I 108 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY J  39 " --> pdb=" O   LEU J  35 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 43 through 50
    Processing helix  chain 'J' and resid 58 through 67
    Processing helix  chain 'J' and resid 69 through 82
    Processing helix  chain 'J' and resid 90 through 104
    Processing helix  chain 'J' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG J 112 " --> pdb=" O   LYS J 108 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3078
        1.34 -     1.46: 1455
        1.46 -     1.57: 5127
        1.57 -     1.69: 0
        1.69 -     1.80: 60
  Bond restraints: 9720
  Sorted by residual:
  bond pdb=" CA  THR F 106 "
       pdb=" CB  THR F 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.46e+00
  bond pdb=" CA  THR J 106 "
       pdb=" CB  THR J 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.42e+00
  bond pdb=" CA  THR I 106 "
       pdb=" CB  THR I 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.42e+00
  bond pdb=" CA  THR E 106 "
       pdb=" CB  THR E 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.025 2.15e-02 2.16e+03 1.41e+00
  bond pdb=" CA  THR B 106 "
       pdb=" CB  THR B 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.025 2.15e-02 2.16e+03 1.40e+00
  ... (remaining 9715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 11927
        1.32 -     2.64: 933
        2.64 -     3.96: 207
        3.96 -     5.28: 59
        5.28 -     6.60: 14
  Bond angle restraints: 13140
  Sorted by residual:
  angle pdb=" N   ILE D 125 "
        pdb=" CA  ILE D 125 "
        pdb=" C   ILE D 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.23    3.54 1.04e+00 9.25e-01 1.16e+01
  angle pdb=" N   ILE C 125 "
        pdb=" CA  ILE C 125 "
        pdb=" C   ILE C 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.24    3.53 1.04e+00 9.25e-01 1.15e+01
  angle pdb=" N   ILE G 125 "
        pdb=" CA  ILE G 125 "
        pdb=" C   ILE G 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.25    3.52 1.04e+00 9.25e-01 1.15e+01
  angle pdb=" N   ILE E 125 "
        pdb=" CA  ILE E 125 "
        pdb=" C   ILE E 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.26    3.51 1.04e+00 9.25e-01 1.14e+01
  angle pdb=" N   ILE H 125 "
        pdb=" CA  ILE H 125 "
        pdb=" C   ILE H 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.26    3.51 1.04e+00 9.25e-01 1.14e+01
  ... (remaining 13135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.87: 4239
       11.87 -    23.74: 839
       23.74 -    35.61: 492
       35.61 -    47.48: 187
       47.48 -    59.35: 93
  Dihedral angle restraints: 5850
    sinusoidal: 2430
      harmonic: 3420
  Sorted by residual:
  dihedral pdb=" CA  GLU C 124 "
           pdb=" C   GLU C 124 "
           pdb=" N   ILE C 125 "
           pdb=" CA  ILE C 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  GLU H 124 "
           pdb=" C   GLU H 124 "
           pdb=" N   ILE H 125 "
           pdb=" CA  ILE H 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  GLU I 124 "
           pdb=" C   GLU I 124 "
           pdb=" N   ILE I 125 "
           pdb=" CA  ILE I 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 686
       0.024 -    0.048: 387
       0.048 -    0.071: 224
       0.071 -    0.095: 73
       0.095 -    0.119: 20
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  ILE D 125 "
            pdb=" N   ILE D 125 "
            pdb=" C   ILE D 125 "
            pdb=" CB  ILE D 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality pdb=" CA  ILE E 125 "
            pdb=" N   ILE E 125 "
            pdb=" C   ILE E 125 "
            pdb=" CB  ILE E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  ILE J 125 "
            pdb=" N   ILE J 125 "
            pdb=" C   ILE J 125 "
            pdb=" CB  ILE J 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.35e-01
  ... (remaining 1387 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR J 106 "   -0.013 2.00e-02 2.50e+03   2.50e-02 6.24e+00
        pdb=" C   THR J 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR J 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL J 107 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F 106 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" C   THR F 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR F 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL F 107 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 106 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   THR H 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR H 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL H 107 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 90
        2.60 -     3.18: 8187
        3.18 -     3.75: 14095
        3.75 -     4.33: 18161
        4.33 -     4.90: 30697
  Nonbonded interactions: 71230
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  61 "
            pdb=" NH2 ARG D  44 "
     model   vdw
     2.026 3.120
  nonbonded pdb=" O   ALA H  61 "
            pdb=" NH2 ARG I  44 "
     model   vdw
     2.027 3.120
  nonbonded pdb=" O   ALA E  61 "
            pdb=" NH2 ARG F  44 "
     model   vdw
     2.059 3.120
  nonbonded pdb=" NH2 ARG A  44 "
            pdb=" O   ALA J  61 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" O   ALA B  61 "
            pdb=" NH2 ARG C  44 "
     model   vdw
     2.083 3.120
  ... (remaining 71225 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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 individual isotropic
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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     21.100
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
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   0.036   9720  Z= 0.293
  Angle     :  0.863   6.601  13140  Z= 0.519
  Chirality :  0.039   0.119   1390
  Planarity :  0.005   0.025   1690
  Dihedral  : 19.495  59.348   3610
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.16 %
    Favored  : 85.84 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 34.10 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.24), residues: 1130
  helix: -0.30 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -5.50 (0.18), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  50 
 HIS   0.002   0.001   HIS I  54 
 PHE   0.008   0.001   PHE D  64 
 TYR   0.022   0.003   TYR J  40 
 ARG   0.009   0.001   ARG F  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A   54 HIS cc_start: 0.6975 (m-70) cc_final: 0.6501 (m-70)
REVERT: B   38 GLN cc_start: 0.8494 (tp40) cc_final: 0.8232 (tp-100)
REVERT: B   54 HIS cc_start: 0.7007 (m-70) cc_final: 0.6580 (m-70)
REVERT: B   77 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7612 (tttp)
REVERT: D   38 GLN cc_start: 0.8546 (tp40) cc_final: 0.8228 (tp-100)
REVERT: D   54 HIS cc_start: 0.7001 (m-70) cc_final: 0.6531 (m-70)
REVERT: D   77 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7719 (ttmm)
REVERT: F   54 HIS cc_start: 0.7045 (m-70) cc_final: 0.6580 (m-70)
REVERT: G   38 GLN cc_start: 0.8473 (tp40) cc_final: 0.8220 (tp-100)
REVERT: G   54 HIS cc_start: 0.7002 (m-70) cc_final: 0.6580 (m-70)
REVERT: I   38 GLN cc_start: 0.8437 (tp40) cc_final: 0.8198 (tp40)
REVERT: I   54 HIS cc_start: 0.6948 (m-70) cc_final: 0.6474 (m-70)
REVERT: I   77 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7637 (ttmm)
REVERT: I  101 MET cc_start: 0.8789 (ttp) cc_final: 0.8579 (ttp)
REVERT: J   54 HIS cc_start: 0.6827 (m-70) cc_final: 0.6495 (m-70)
  outliers start: 20
  outliers final: 0
  residues processed: 231
  average time/residue: 0.3385
  time to fit residues: 97.5082
Evaluate side-chains
  193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.0770
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.3942

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

Flipped N/Q/H residues before XYZ refinement:
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.173231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127931 restraints weight = 10710.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.83
r_work: 0.3281 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9720  Z= 0.244
  Angle     :  0.675   4.408  13140  Z= 0.368
  Chirality :  0.039   0.125   1390
  Planarity :  0.006   0.063   1690
  Dihedral  :  5.430  17.280   1260
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.72 %
    Favored  : 86.28 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.00 %
    Favored  : 68.00 %
  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: -1.87 (0.24), residues: 1130
  helix:  0.37 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.38 (0.21), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E  50 
 HIS   0.002   0.001   HIS B  96 
 PHE   0.011   0.001   PHE J  64 
 TYR   0.017   0.002   TYR C  40 
 ARG   0.009   0.001   ARG A  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 218
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A   54 HIS cc_start: 0.6685 (m-70) cc_final: 0.6399 (m-70)
REVERT: B   54 HIS cc_start: 0.6698 (m-70) cc_final: 0.6487 (m-70)
REVERT: B   63 ILE cc_start: 0.8711 (mt) cc_final: 0.8503 (mp)
REVERT: B   73 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6848 (mtm180)
REVERT: B   77 LYS cc_start: 0.7522 (mtpt) cc_final: 0.7256 (tttp)
REVERT: B  122 LEU cc_start: 0.8612 (mt) cc_final: 0.8237 (tt)
REVERT: C  122 LEU cc_start: 0.8733 (mt) cc_final: 0.8250 (tt)
REVERT: D   54 HIS cc_start: 0.6685 (m-70) cc_final: 0.6293 (m-70)
REVERT: E   38 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8046 (tp-100)
REVERT: E  122 LEU cc_start: 0.8539 (mt) cc_final: 0.8292 (tt)
REVERT: F   54 HIS cc_start: 0.6799 (m-70) cc_final: 0.6467 (m-70)
REVERT: F   73 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6825 (mtm180)
REVERT: F  122 LEU cc_start: 0.8560 (mt) cc_final: 0.8319 (tt)
REVERT: G   54 HIS cc_start: 0.6718 (m-70) cc_final: 0.6490 (m-70)
REVERT: G   63 ILE cc_start: 0.8705 (mt) cc_final: 0.8495 (mp)
REVERT: G   73 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6736 (mtm180)
REVERT: G  122 LEU cc_start: 0.8630 (mt) cc_final: 0.8241 (tt)
REVERT: H  122 LEU cc_start: 0.8717 (mt) cc_final: 0.8256 (tt)
REVERT: I   54 HIS cc_start: 0.6682 (m-70) cc_final: 0.6316 (m-70)
REVERT: I   77 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7331 (ttmm)
REVERT: J   38 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8039 (tp-100)
REVERT: J  122 LEU cc_start: 0.8587 (mt) cc_final: 0.8309 (tt)
  outliers start: 40
  outliers final: 8
  residues processed: 250
  average time/residue: 0.2914
  time to fit residues: 92.6470
Evaluate side-chains
  211 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   73 ARG
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain J residue   18 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0060
   chunk 90 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 80 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.176722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.135011 restraints weight = 10733.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.58
r_work: 0.3365 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9720  Z= 0.194
  Angle     :  0.622   5.536  13140  Z= 0.336
  Chirality :  0.037   0.122   1390
  Planarity :  0.006   0.068   1690
  Dihedral  :  5.181  16.511   1260
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.25 %
    Favored  : 85.75 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.50 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 1130
  helix:  0.92 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.37 (0.20), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J  50 
 HIS   0.002   0.000   HIS B  96 
 PHE   0.015   0.001   PHE C  64 
 TYR   0.018   0.002   TYR C  40 
 ARG   0.006   0.001   ARG J  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 204
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.6588 (m-70) cc_final: 0.6256 (m-70)
REVERT: A   81 ASN cc_start: 0.8919 (m-40) cc_final: 0.8691 (m-40)
REVERT: A  122 LEU cc_start: 0.8488 (mt) cc_final: 0.8202 (tt)
REVERT: B   54 HIS cc_start: 0.6629 (m-70) cc_final: 0.6352 (m-70)
REVERT: B   77 LYS cc_start: 0.7386 (mtpt) cc_final: 0.7112 (tttp)
REVERT: B  122 LEU cc_start: 0.8549 (mt) cc_final: 0.8207 (tt)
REVERT: C  122 LEU cc_start: 0.8667 (mt) cc_final: 0.8218 (tt)
REVERT: D   54 HIS cc_start: 0.6670 (m-70) cc_final: 0.6353 (m-70)
REVERT: D   62 ARG cc_start: 0.8281 (tpt170) cc_final: 0.8066 (tmt-80)
REVERT: E   38 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7969 (tp-100)
REVERT: E   73 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6727 (mtm180)
REVERT: E  122 LEU cc_start: 0.8565 (mt) cc_final: 0.8288 (tt)
REVERT: F   54 HIS cc_start: 0.6708 (m-70) cc_final: 0.6362 (m-70)
REVERT: F  122 LEU cc_start: 0.8487 (mt) cc_final: 0.8217 (tt)
REVERT: G   54 HIS cc_start: 0.6644 (m-70) cc_final: 0.6383 (m-70)
REVERT: G  122 LEU cc_start: 0.8552 (mt) cc_final: 0.8192 (tt)
REVERT: H  122 LEU cc_start: 0.8649 (mt) cc_final: 0.8224 (tt)
REVERT: I   54 HIS cc_start: 0.6606 (m-70) cc_final: 0.6254 (m-70)
REVERT: I   62 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7972 (tmt-80)
REVERT: I   73 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6615 (mtm180)
REVERT: J  122 LEU cc_start: 0.8577 (mt) cc_final: 0.8266 (tt)
  outliers start: 46
  outliers final: 22
  residues processed: 231
  average time/residue: 0.2853
  time to fit residues: 84.2930
Evaluate side-chains
  219 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain E residue   73 ARG
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue  127 PHE
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   18 ASP
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  127 PHE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   73 ARG
Chi-restraints excluded: chain I residue  127 PHE
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 100 GLN
** J  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.174960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129234 restraints weight = 10942.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.98
r_work: 0.3223 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9720  Z= 0.255
  Angle     :  0.644   5.200  13140  Z= 0.345
  Chirality :  0.038   0.145   1390
  Planarity :  0.006   0.065   1690
  Dihedral  :  5.183  15.934   1260
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.78 %
    Favored  : 85.22 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 27.20 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1130
  helix:  1.25 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.26 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  50 
 HIS   0.002   0.001   HIS D  96 
 PHE   0.019   0.002   PHE J  64 
 TYR   0.012   0.002   TYR G  40 
 ARG   0.004   0.001   ARG B  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 190
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8960 (m-40) cc_final: 0.8741 (m-40)
REVERT: A  122 LEU cc_start: 0.8547 (mt) cc_final: 0.8269 (tt)
REVERT: B   73 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6577 (mtm180)
REVERT: B   77 LYS cc_start: 0.7352 (mtpt) cc_final: 0.7103 (ttmm)
REVERT: B  122 LEU cc_start: 0.8548 (mt) cc_final: 0.8198 (tt)
REVERT: C   73 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6664 (mtm180)
REVERT: C  122 LEU cc_start: 0.8576 (mt) cc_final: 0.8138 (tt)
REVERT: D   54 HIS cc_start: 0.6656 (m-70) cc_final: 0.6191 (m-70)
REVERT: D   62 ARG cc_start: 0.8283 (tpt170) cc_final: 0.8056 (tmt-80)
REVERT: E   38 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7911 (tp-100)
REVERT: E  122 LEU cc_start: 0.8537 (mt) cc_final: 0.8260 (tt)
REVERT: F   73 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6672 (mtp180)
REVERT: F  122 LEU cc_start: 0.8534 (mt) cc_final: 0.8272 (tt)
REVERT: G   54 HIS cc_start: 0.6742 (m-70) cc_final: 0.6414 (m-70)
REVERT: G  122 LEU cc_start: 0.8556 (mt) cc_final: 0.8212 (tt)
REVERT: H   73 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6678 (mtm180)
REVERT: H  122 LEU cc_start: 0.8604 (mt) cc_final: 0.8176 (tt)
REVERT: I   54 HIS cc_start: 0.6613 (m-70) cc_final: 0.6179 (m-70)
REVERT: I   62 ARG cc_start: 0.8296 (tpt170) cc_final: 0.8030 (tmt-80)
REVERT: J   38 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7887 (tp-100)
REVERT: J   73 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6658 (mtm180)
REVERT: J  122 LEU cc_start: 0.8567 (mt) cc_final: 0.8224 (tt)
  outliers start: 47
  outliers final: 20
  residues processed: 216
  average time/residue: 0.3395
  time to fit residues: 92.3511
Evaluate side-chains
  209 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   18 ASP
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   18 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue  127 PHE
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   73 ARG
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0980
   chunk 62 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 38 optimal weight:    8.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
H  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.179190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.133403 restraints weight = 10751.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.00
r_work: 0.3265 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9720  Z= 0.174
  Angle     :  0.586   6.040  13140  Z= 0.315
  Chirality :  0.037   0.152   1390
  Planarity :  0.004   0.025   1690
  Dihedral  :  4.813  15.322   1260
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.07 %
    Favored  : 85.93 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.70 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1130
  helix:  1.67 (0.19), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.28 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J  50 
 HIS   0.002   0.000   HIS J  54 
 PHE   0.009   0.001   PHE C  64 
 TYR   0.014   0.001   TYR H  40 
 ARG   0.003   0.000   ARG C  36 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 192
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8951 (m-40) cc_final: 0.8703 (m-40)
REVERT: A  122 LEU cc_start: 0.8497 (mt) cc_final: 0.8176 (tt)
REVERT: B   55 MET cc_start: 0.7029 (mmm) cc_final: 0.6809 (mmp)
REVERT: B   77 LYS cc_start: 0.7372 (mtpt) cc_final: 0.7096 (ttmm)
REVERT: B  122 LEU cc_start: 0.8504 (mt) cc_final: 0.8232 (tt)
REVERT: C  122 LEU cc_start: 0.8473 (mt) cc_final: 0.8136 (tt)
REVERT: D   18 ASP cc_start: 0.6672 (m-30) cc_final: 0.6311 (p0)
REVERT: D   54 HIS cc_start: 0.6666 (m-70) cc_final: 0.6229 (m-70)
REVERT: D  109 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7374 (m-30)
REVERT: F  109 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7410 (m-30)
REVERT: F  122 LEU cc_start: 0.8505 (mt) cc_final: 0.8187 (tt)
REVERT: G   55 MET cc_start: 0.7018 (mmm) cc_final: 0.6815 (mmp)
REVERT: G  122 LEU cc_start: 0.8497 (mt) cc_final: 0.8225 (tt)
REVERT: H   55 MET cc_start: 0.7125 (mmm) cc_final: 0.6923 (mmp)
REVERT: H  122 LEU cc_start: 0.8475 (mt) cc_final: 0.8154 (tt)
REVERT: I   54 HIS cc_start: 0.6586 (m-70) cc_final: 0.6185 (m-70)
REVERT: I   62 ARG cc_start: 0.8270 (tpt170) cc_final: 0.8031 (tpt170)
REVERT: I  109 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7326 (m-30)
REVERT: J  122 LEU cc_start: 0.8478 (mt) cc_final: 0.8266 (tt)
  outliers start: 39
  outliers final: 25
  residues processed: 221
  average time/residue: 0.2190
  time to fit residues: 65.9702
Evaluate side-chains
  208 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  109 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  109 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  127 PHE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  109 ASP
Chi-restraints excluded: chain I residue  127 PHE
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.179724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.134493 restraints weight = 10883.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.01
r_work: 0.3253 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9720  Z= 0.196
  Angle     :  0.592   6.570  13140  Z= 0.317
  Chirality :  0.038   0.181   1390
  Planarity :  0.003   0.028   1690
  Dihedral  :  4.660  14.935   1260
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.78 %
    Favored  : 85.22 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.60 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1130
  helix:  1.83 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.17 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  50 
 HIS   0.002   0.001   HIS J  54 
 PHE   0.008   0.001   PHE C  64 
 TYR   0.010   0.002   TYR G  72 
 ARG   0.002   0.000   ARG D  62 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 1.101 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6552 (mtm180)
REVERT: A   81 ASN cc_start: 0.9013 (m-40) cc_final: 0.8782 (m-40)
REVERT: A  122 LEU cc_start: 0.8539 (mt) cc_final: 0.8266 (tt)
REVERT: B   73 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6603 (mtm180)
REVERT: B  122 LEU cc_start: 0.8521 (mt) cc_final: 0.8282 (tt)
REVERT: C   73 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6584 (mtm180)
REVERT: C  122 LEU cc_start: 0.8471 (mt) cc_final: 0.8141 (tt)
REVERT: D   18 ASP cc_start: 0.6697 (m-30) cc_final: 0.6359 (p0)
REVERT: D   55 MET cc_start: 0.7270 (mmm) cc_final: 0.7046 (mmp)
REVERT: D  109 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7447 (m-30)
REVERT: D  113 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: F  122 LEU cc_start: 0.8541 (mt) cc_final: 0.8269 (tt)
REVERT: G  122 LEU cc_start: 0.8548 (mt) cc_final: 0.8287 (tt)
REVERT: H   73 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6674 (mtm180)
REVERT: H  122 LEU cc_start: 0.8464 (mt) cc_final: 0.8153 (tt)
REVERT: I   18 ASP cc_start: 0.6672 (m-30) cc_final: 0.6330 (p0)
REVERT: I   55 MET cc_start: 0.7261 (mmm) cc_final: 0.7040 (mmp)
REVERT: I   62 ARG cc_start: 0.8330 (tpt170) cc_final: 0.8108 (tpt170)
REVERT: J   73 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6605 (mtm180)
  outliers start: 42
  outliers final: 18
  residues processed: 212
  average time/residue: 0.2584
  time to fit residues: 72.5488
Evaluate side-chains
  205 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  109 ASP
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   73 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0670
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.5322

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.168082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.122057 restraints weight = 10893.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.90
r_work: 0.3202 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9720  Z= 0.231
  Angle     :  0.635   7.175  13140  Z= 0.339
  Chirality :  0.041   0.214   1390
  Planarity :  0.003   0.029   1690
  Dihedral  :  4.680  15.478   1260
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.78 %
    Favored  : 85.22 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 26.30 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1130
  helix:  1.86 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.09 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  50 
 HIS   0.003   0.001   HIS J  54 
 PHE   0.008   0.001   PHE C  64 
 TYR   0.010   0.002   TYR D  72 
 ARG   0.002   0.000   ARG F  62 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6546 (mtp180)
REVERT: A   81 ASN cc_start: 0.9023 (m-40) cc_final: 0.8796 (m-40)
REVERT: A  122 LEU cc_start: 0.8557 (mt) cc_final: 0.8294 (tt)
REVERT: B   55 MET cc_start: 0.6948 (mmm) cc_final: 0.6575 (mmp)
REVERT: B  122 LEU cc_start: 0.8496 (mt) cc_final: 0.8250 (tt)
REVERT: C   73 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6702 (mtm180)
REVERT: C  122 LEU cc_start: 0.8505 (mt) cc_final: 0.8134 (tt)
REVERT: D   18 ASP cc_start: 0.6751 (m-30) cc_final: 0.6439 (p0)
REVERT: D   55 MET cc_start: 0.7266 (mmm) cc_final: 0.7061 (mmp)
REVERT: D  113 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8038 (tp)
REVERT: F   66 MET cc_start: 0.9021 (tmm) cc_final: 0.8508 (tmm)
REVERT: F   73 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6606 (mtp180)
REVERT: F  122 LEU cc_start: 0.8541 (mt) cc_final: 0.8274 (tt)
REVERT: G   55 MET cc_start: 0.6799 (mmm) cc_final: 0.6553 (mmp)
REVERT: G  122 LEU cc_start: 0.8541 (mt) cc_final: 0.8274 (tt)
REVERT: H  122 LEU cc_start: 0.8475 (mt) cc_final: 0.8168 (tt)
REVERT: I   18 ASP cc_start: 0.6725 (m-30) cc_final: 0.6405 (p0)
REVERT: I   55 MET cc_start: 0.7291 (mmm) cc_final: 0.7078 (mmp)
REVERT: I   62 ARG cc_start: 0.8326 (tpt170) cc_final: 0.8080 (tpt170)
  outliers start: 27
  outliers final: 14
  residues processed: 196
  average time/residue: 0.3143
  time to fit residues: 80.6774
Evaluate side-chains
  196 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.175040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.130430 restraints weight = 11062.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.99
r_work: 0.3189 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9720  Z= 0.241
  Angle     :  0.638   7.520  13140  Z= 0.344
  Chirality :  0.042   0.222   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.720  15.698   1260
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 26.20 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1130
  helix:  1.89 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.00 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP J  50 
 HIS   0.002   0.001   HIS F  20 
 PHE   0.008   0.001   PHE C  64 
 TYR   0.010   0.002   TYR J  72 
 ARG   0.004   0.000   ARG J  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 1.133 
Fit side-chains
REVERT: A   66 MET cc_start: 0.9028 (tmm) cc_final: 0.8544 (tmm)
REVERT: A   73 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6607 (mtp180)
REVERT: A   81 ASN cc_start: 0.8979 (m-40) cc_final: 0.8747 (m-40)
REVERT: A  122 LEU cc_start: 0.8587 (mt) cc_final: 0.8327 (tt)
REVERT: B   55 MET cc_start: 0.7112 (mmm) cc_final: 0.6834 (mmp)
REVERT: B   73 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6587 (mtm180)
REVERT: B  122 LEU cc_start: 0.8579 (mt) cc_final: 0.8286 (tt)
REVERT: C   73 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6750 (mtm180)
REVERT: C  122 LEU cc_start: 0.8557 (mt) cc_final: 0.8219 (tt)
REVERT: D  113 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8154 (tp)
REVERT: F   66 MET cc_start: 0.9010 (tmm) cc_final: 0.8525 (tmm)
REVERT: F   73 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6599 (mtm180)
REVERT: F  122 LEU cc_start: 0.8598 (mt) cc_final: 0.8334 (tt)
REVERT: G   55 MET cc_start: 0.6927 (mmm) cc_final: 0.6721 (mmp)
REVERT: G  122 LEU cc_start: 0.8541 (mt) cc_final: 0.8240 (tt)
REVERT: H   73 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6723 (mtm180)
REVERT: H  122 LEU cc_start: 0.8530 (mt) cc_final: 0.8181 (tt)
REVERT: I   62 ARG cc_start: 0.8371 (tpt170) cc_final: 0.8112 (tpt170)
  outliers start: 27
  outliers final: 12
  residues processed: 196
  average time/residue: 0.3756
  time to fit residues: 95.4352
Evaluate side-chains
  195 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.177858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.133775 restraints weight = 10908.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.99
r_work: 0.3230 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9720  Z= 0.195
  Angle     :  0.634   8.048  13140  Z= 0.343
  Chirality :  0.041   0.218   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.614  16.025   1260
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.27 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 26.70 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.26), residues: 1130
  helix:  1.90 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.94 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP J  43 
 HIS   0.003   0.000   HIS I  20 
 PHE   0.006   0.001   PHE C  64 
 TYR   0.009   0.001   TYR I  40 
 ARG   0.002   0.000   ARG C  36 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   18 ASP cc_start: 0.6882 (t0) cc_final: 0.6554 (t70)
REVERT: A   66 MET cc_start: 0.8949 (tmm) cc_final: 0.8488 (tmm)
REVERT: A   73 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6525 (mtp180)
REVERT: A   81 ASN cc_start: 0.9031 (m-40) cc_final: 0.8805 (m-40)
REVERT: A  122 LEU cc_start: 0.8549 (mt) cc_final: 0.8318 (tt)
REVERT: B  122 LEU cc_start: 0.8544 (mt) cc_final: 0.8298 (tt)
REVERT: C  122 LEU cc_start: 0.8449 (mt) cc_final: 0.8181 (tt)
REVERT: D   55 MET cc_start: 0.6681 (mmp) cc_final: 0.6463 (mmm)
REVERT: D  113 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: E   50 TRP cc_start: 0.8471 (m100) cc_final: 0.8186 (m100)
REVERT: F   66 MET cc_start: 0.8986 (tmm) cc_final: 0.8538 (tmm)
REVERT: F   73 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6521 (mtm180)
REVERT: F  122 LEU cc_start: 0.8517 (mt) cc_final: 0.8291 (tt)
REVERT: G  122 LEU cc_start: 0.8532 (mt) cc_final: 0.8276 (tt)
REVERT: H   73 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6796 (mtm180)
REVERT: H  122 LEU cc_start: 0.8506 (mt) cc_final: 0.8257 (tt)
REVERT: I   62 ARG cc_start: 0.8313 (tpt170) cc_final: 0.8059 (tpt170)
  outliers start: 18
  outliers final: 13
  residues processed: 199
  average time/residue: 0.2974
  time to fit residues: 75.5046
Evaluate side-chains
  198 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0060
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.0000

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

Flipped N/Q/H residues before XYZ refinement:
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.171223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125157 restraints weight = 11012.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.04
r_work: 0.3230 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9720  Z= 0.214
  Angle     :  0.643   8.527  13140  Z= 0.351
  Chirality :  0.042   0.228   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.560  16.713   1260
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.36 %
    Favored  : 86.64 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 26.90 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1130
  helix:  1.84 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.93 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E  43 
 HIS   0.003   0.001   HIS E  54 
 PHE   0.007   0.001   PHE G  64 
 TYR   0.019   0.002   TYR B  72 
 ARG   0.003   0.000   ARG E  44 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 1.211 
Fit side-chains
REVERT: A   66 MET cc_start: 0.8989 (tmm) cc_final: 0.8524 (tmm)
REVERT: A   73 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6547 (mtm180)
REVERT: A   81 ASN cc_start: 0.9028 (m-40) cc_final: 0.8811 (m-40)
REVERT: A  122 LEU cc_start: 0.8485 (mt) cc_final: 0.8267 (tt)
REVERT: B   55 MET cc_start: 0.6939 (mmp) cc_final: 0.6736 (mmm)
REVERT: B   73 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6580 (mtm180)
REVERT: B  122 LEU cc_start: 0.8655 (mt) cc_final: 0.8343 (tt)
REVERT: C  122 LEU cc_start: 0.8490 (mt) cc_final: 0.8253 (tt)
REVERT: D   55 MET cc_start: 0.6715 (mmp) cc_final: 0.6499 (mmm)
REVERT: D  113 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (tp)
REVERT: E   55 MET cc_start: 0.6864 (mmm) cc_final: 0.6640 (mmp)
REVERT: F   66 MET cc_start: 0.9009 (tmm) cc_final: 0.8546 (tmm)
REVERT: F   73 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6545 (mtm180)
REVERT: F  122 LEU cc_start: 0.8508 (mt) cc_final: 0.8300 (tt)
REVERT: G   55 MET cc_start: 0.6674 (mmp) cc_final: 0.6449 (mmm)
REVERT: G  122 LEU cc_start: 0.8572 (mt) cc_final: 0.8332 (tt)
REVERT: H  122 LEU cc_start: 0.8490 (mt) cc_final: 0.8277 (tt)
REVERT: I   55 MET cc_start: 0.6999 (mmm) cc_final: 0.6755 (mmp)
REVERT: I   62 ARG cc_start: 0.8335 (tpt170) cc_final: 0.8095 (tpt170)
REVERT: J   55 MET cc_start: 0.6868 (mmm) cc_final: 0.6641 (mmp)
  outliers start: 20
  outliers final: 16
  residues processed: 193
  average time/residue: 0.3219
  time to fit residues: 80.4882
Evaluate side-chains
  198 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.171751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.126395 restraints weight = 10937.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 3.00
r_work: 0.3274 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9720  Z= 0.212
  Angle     :  0.654   8.718  13140  Z= 0.356
  Chirality :  0.041   0.219   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.547  16.869   1260
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.27 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 27.30 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1130
  helix:  1.82 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.88 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  43 
 HIS   0.002   0.000   HIS C  54 
 PHE   0.008   0.001   PHE B  64 
 TYR   0.017   0.002   TYR B  72 
 ARG   0.002   0.000   ARG A  36 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4106.23 seconds
wall clock time: 72 minutes 8.88 seconds (4328.88 seconds total)