Starting phenix.real_space_refine
on Sat Dec 28 21:42:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uxe_26858/12_2024/7uxe_26858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxe_26858/12_2024/7uxe_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_26858/12_2024/7uxe_26858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxe_26858/12_2024/7uxe_26858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxe_26858/12_2024/7uxe_26858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxe_26858/12_2024/7uxe_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-5532/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: 2.95, per 1000 atoms: 0.31
  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: 2.57
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.77
  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: 2.31

  Time building geometry restraints manager: 2.91 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     20.040
  Find NCS groups from input model:        0.320
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.190
-------------------------------------------------------------------------------
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  : 0.960 
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: 0.3812
  time to fit residues: 110.7377
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  : 1.178 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
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  : 1.152 
Fit side-chains
REVERT: A   54 HIS cc_start: 0.6940 (m-70) cc_final: 0.6646 (m-70)
REVERT: B   54 HIS cc_start: 0.6941 (m-70) cc_final: 0.6694 (m-70)
REVERT: B   62 ARG cc_start: 0.8547 (tpt170) cc_final: 0.8339 (tpt170)
REVERT: B   73 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7066 (mtm180)
REVERT: B   77 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7539 (tttp)
REVERT: B  122 LEU cc_start: 0.8527 (mt) cc_final: 0.8180 (tt)
REVERT: C   54 HIS cc_start: 0.6708 (m-70) cc_final: 0.6495 (m-70)
REVERT: C  122 LEU cc_start: 0.8639 (mt) cc_final: 0.8195 (tt)
REVERT: D   54 HIS cc_start: 0.6983 (m-70) cc_final: 0.6556 (m-70)
REVERT: D   77 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7815 (ttmm)
REVERT: E   38 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8102 (tp-100)
REVERT: E  122 LEU cc_start: 0.8480 (mt) cc_final: 0.8253 (tt)
REVERT: F   54 HIS cc_start: 0.7068 (m-70) cc_final: 0.6734 (m-70)
REVERT: F   73 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7033 (mtm180)
REVERT: F  122 LEU cc_start: 0.8500 (mt) cc_final: 0.8287 (tt)
REVERT: G   54 HIS cc_start: 0.6968 (m-70) cc_final: 0.6718 (m-70)
REVERT: G   62 ARG cc_start: 0.8532 (tpt170) cc_final: 0.8328 (tpt170)
REVERT: G   73 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6965 (mtm180)
REVERT: G  122 LEU cc_start: 0.8532 (mt) cc_final: 0.8171 (tt)
REVERT: H  122 LEU cc_start: 0.8620 (mt) cc_final: 0.8196 (tt)
REVERT: I   54 HIS cc_start: 0.6960 (m-70) cc_final: 0.6570 (m-70)
REVERT: I   77 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7626 (ttmm)
REVERT: J   38 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8085 (tp-100)
REVERT: J   54 HIS cc_start: 0.6768 (m-70) cc_final: 0.6528 (m-70)
REVERT: J  122 LEU cc_start: 0.8520 (mt) cc_final: 0.8266 (tt)
  outliers start: 40
  outliers final: 8
  residues processed: 250
  average time/residue: 0.3052
  time to fit residues: 96.6042
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  : 1.083 
-------------------------------------------------------------------------------
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 55 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0010
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
J 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2452

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= 0.198
  Angle     :  0.626   5.625  13140  Z= 0.339
  Chirality :  0.037   0.120   1390
  Planarity :  0.006   0.065   1690
  Dihedral  :  5.183  16.455   1260
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.51 %
    Favored  : 85.49 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 28.10 %
    Favored  : 67.40 %
  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: -1.24 (0.25), residues: 1130
  helix:  0.92 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.35 (0.21), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  50 
 HIS   0.002   0.000   HIS B  96 
 PHE   0.015   0.001   PHE E  64 
 TYR   0.018   0.002   TYR C  40 
 ARG   0.005   0.001   ARG G  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
  247 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 202
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.6952 (m-70) cc_final: 0.6591 (m-70)
REVERT: A  122 LEU cc_start: 0.8507 (mt) cc_final: 0.8257 (tt)
REVERT: B   54 HIS cc_start: 0.7023 (m-70) cc_final: 0.6726 (m-70)
REVERT: B   77 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7534 (tttp)
REVERT: B  122 LEU cc_start: 0.8538 (mt) cc_final: 0.8231 (tt)
REVERT: C   40 TYR cc_start: 0.8497 (m-80) cc_final: 0.8288 (m-80)
REVERT: C  122 LEU cc_start: 0.8680 (mt) cc_final: 0.8256 (tt)
REVERT: D   54 HIS cc_start: 0.7017 (m-70) cc_final: 0.6642 (m-70)
REVERT: D   62 ARG cc_start: 0.8608 (tpt170) cc_final: 0.8396 (tmt-80)
REVERT: D   77 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7782 (ttmm)
REVERT: E   73 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7065 (mtm180)
REVERT: E  122 LEU cc_start: 0.8612 (mt) cc_final: 0.8361 (tt)
REVERT: F   54 HIS cc_start: 0.6959 (m-70) cc_final: 0.6609 (m-70)
REVERT: F  122 LEU cc_start: 0.8501 (mt) cc_final: 0.8268 (tt)
REVERT: G   54 HIS cc_start: 0.7034 (m-70) cc_final: 0.6729 (m-70)
REVERT: G  122 LEU cc_start: 0.8536 (mt) cc_final: 0.8214 (tt)
REVERT: H  122 LEU cc_start: 0.8675 (mt) cc_final: 0.8267 (tt)
REVERT: I   54 HIS cc_start: 0.6946 (m-70) cc_final: 0.6527 (m-70)
REVERT: I   62 ARG cc_start: 0.8574 (tpt170) cc_final: 0.8311 (tmt-80)
REVERT: I   73 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6961 (mtm180)
REVERT: I   77 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7614 (ttmm)
REVERT: J  122 LEU cc_start: 0.8620 (mt) cc_final: 0.8313 (tt)
  outliers start: 45
  outliers final: 24
  residues processed: 227
  average time/residue: 0.3248
  time to fit residues: 93.9458
Evaluate side-chains
  219 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
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 E residue  127 PHE
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   18 ASP
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 98 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 11 optimal weight:   20.0000
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2864

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= 0.193
  Angle     :  0.607   5.515  13140  Z= 0.328
  Chirality :  0.036   0.161   1390
  Planarity :  0.006   0.064   1690
  Dihedral  :  5.048  16.129   1260
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.25 %
    Favored  : 85.75 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 27.10 %
    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: -0.82 (0.26), residues: 1130
  helix:  1.28 (0.19), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.31 (0.21), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  50 
 HIS   0.002   0.000   HIS D  96 
 PHE   0.014   0.001   PHE B  64 
 TYR   0.017   0.002   TYR E  40 
 ARG   0.003   0.000   ARG E  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
  244 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 194
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7519 (m-30)
REVERT: A  122 LEU cc_start: 0.8598 (mt) cc_final: 0.8325 (tt)
REVERT: B   73 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6890 (mtm180)
REVERT: B   77 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7484 (tttp)
REVERT: B  122 LEU cc_start: 0.8522 (mt) cc_final: 0.8271 (tt)
REVERT: C   40 TYR cc_start: 0.8501 (m-80) cc_final: 0.8287 (m-80)
REVERT: C   55 MET cc_start: 0.7023 (mmm) cc_final: 0.6726 (mmp)
REVERT: C   73 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6849 (mtm180)
REVERT: C  122 LEU cc_start: 0.8626 (mt) cc_final: 0.8243 (tt)
REVERT: D   54 HIS cc_start: 0.7022 (m-70) cc_final: 0.6563 (m-70)
REVERT: D   55 MET cc_start: 0.7211 (mmm) cc_final: 0.6965 (mmp)
REVERT: D   62 ARG cc_start: 0.8636 (tpt170) cc_final: 0.8394 (tmt-80)
REVERT: D   77 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7815 (ttmm)
REVERT: E  122 LEU cc_start: 0.8545 (mt) cc_final: 0.8339 (tt)
REVERT: F  109 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: F  122 LEU cc_start: 0.8622 (mt) cc_final: 0.8338 (tt)
REVERT: G  122 LEU cc_start: 0.8529 (mt) cc_final: 0.8266 (tt)
REVERT: H   40 TYR cc_start: 0.8470 (m-80) cc_final: 0.8194 (m-80)
REVERT: H   55 MET cc_start: 0.7135 (mmm) cc_final: 0.6867 (mmp)
REVERT: H   73 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6952 (mtm180)
REVERT: H  122 LEU cc_start: 0.8619 (mt) cc_final: 0.8262 (tt)
REVERT: I   54 HIS cc_start: 0.6889 (m-70) cc_final: 0.6465 (m-70)
REVERT: I   55 MET cc_start: 0.7199 (mmm) cc_final: 0.6949 (mmp)
REVERT: I   62 ARG cc_start: 0.8661 (tpt170) cc_final: 0.8388 (tmt-80)
REVERT: I   77 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7736 (ttmm)
REVERT: J   73 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6995 (mtm180)
REVERT: J  122 LEU cc_start: 0.8565 (mt) cc_final: 0.8337 (tt)
  outliers start: 50
  outliers final: 20
  residues processed: 226
  average time/residue: 0.3257
  time to fit residues: 92.5849
Evaluate side-chains
  214 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 188
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue  109 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   18 ASP
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 C residue  127 PHE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue  109 ASP
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 H residue   99 LEU
Chi-restraints excluded: chain H residue  127 PHE
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0670
   chunk 79 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** E  54 HIS ** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9720  Z= 0.320
  Angle     :  0.667   5.884  13140  Z= 0.358
  Chirality :  0.041   0.162   1390
  Planarity :  0.004   0.028   1690
  Dihedral  :  5.087  16.006   1260
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 27.40 %
    Favored  : 69.00 %
  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: -0.67 (0.26), residues: 1130
  helix:  1.36 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.19 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J  50 
 HIS   0.002   0.001   HIS E  54 
 PHE   0.008   0.001   PHE H  64 
 TYR   0.008   0.002   TYR J  72 
 ARG   0.007   0.001   ARG G  62 

*********************** 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
  221 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6906 (mtm180)
REVERT: A  122 LEU cc_start: 0.8694 (mt) cc_final: 0.8442 (tt)
REVERT: B   55 MET cc_start: 0.7116 (mmm) cc_final: 0.6659 (mmp)
REVERT: B   73 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6968 (mtm180)
REVERT: B   77 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7588 (ttmm)
REVERT: B  122 LEU cc_start: 0.8652 (mt) cc_final: 0.8327 (tt)
REVERT: C   73 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6970 (mtm180)
REVERT: C  122 LEU cc_start: 0.8736 (mt) cc_final: 0.8294 (tt)
REVERT: D   62 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8483 (tpt170)
REVERT: D   73 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6932 (mtm110)
REVERT: D   77 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7785 (ttmm)
REVERT: E  122 LEU cc_start: 0.8647 (mt) cc_final: 0.8399 (tt)
REVERT: F  122 LEU cc_start: 0.8692 (mt) cc_final: 0.8441 (tt)
REVERT: G  122 LEU cc_start: 0.8642 (mt) cc_final: 0.8332 (tt)
REVERT: H   73 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6962 (mtm180)
REVERT: H  122 LEU cc_start: 0.8727 (mt) cc_final: 0.8312 (tt)
REVERT: I   62 ARG cc_start: 0.8737 (tpt170) cc_final: 0.8412 (tpt170)
REVERT: I   77 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7790 (ttmm)
REVERT: J   38 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8125 (tp-100)
REVERT: J  122 LEU cc_start: 0.8674 (mt) cc_final: 0.8406 (tt)
  outliers start: 36
  outliers final: 14
  residues processed: 208
  average time/residue: 0.2943
  time to fit residues: 78.7673
Evaluate side-chains
  201 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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   44 ARG
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain H residue   44 ARG
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   18 ASP
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 35 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
H  38 GLN
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9720  Z= 0.213
  Angle     :  0.620   6.559  13140  Z= 0.332
  Chirality :  0.039   0.180   1390
  Planarity :  0.004   0.025   1690
  Dihedral  :  4.924  15.226   1260
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.07 %
    Favored  : 85.93 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 25.90 %
    Favored  : 69.80 %
  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: -0.39 (0.26), residues: 1130
  helix:  1.60 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.16 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  50 
 HIS   0.002   0.001   HIS C  20 
 PHE   0.009   0.001   PHE F  64 
 TYR   0.013   0.002   TYR H  40 
 ARG   0.003   0.000   ARG E  44 

*********************** 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
  228 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 185
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6849 (mtm180)
REVERT: A  122 LEU cc_start: 0.8678 (mt) cc_final: 0.8454 (tt)
REVERT: B  122 LEU cc_start: 0.8625 (mt) cc_final: 0.8306 (tt)
REVERT: C   55 MET cc_start: 0.6906 (mmm) cc_final: 0.6650 (mmp)
REVERT: C   73 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6994 (mtm180)
REVERT: C  122 LEU cc_start: 0.8648 (mt) cc_final: 0.8249 (tt)
REVERT: D   55 MET cc_start: 0.7232 (mmm) cc_final: 0.6916 (mmp)
REVERT: D   62 ARG cc_start: 0.8723 (tpt170) cc_final: 0.8504 (tpt170)
REVERT: D   77 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7773 (ttmm)
REVERT: E  122 LEU cc_start: 0.8590 (mt) cc_final: 0.8383 (tt)
REVERT: F   73 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7033 (mtm180)
REVERT: F  122 LEU cc_start: 0.8723 (mt) cc_final: 0.8455 (tt)
REVERT: G   55 MET cc_start: 0.6841 (mmm) cc_final: 0.6532 (mmp)
REVERT: G  122 LEU cc_start: 0.8616 (mt) cc_final: 0.8304 (tt)
REVERT: H   55 MET cc_start: 0.6910 (mmm) cc_final: 0.6661 (mmp)
REVERT: H   73 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6998 (mtm180)
REVERT: H  122 LEU cc_start: 0.8617 (mt) cc_final: 0.8238 (tt)
REVERT: I   55 MET cc_start: 0.7249 (mmm) cc_final: 0.6922 (mmp)
REVERT: I   62 ARG cc_start: 0.8738 (tpt170) cc_final: 0.8446 (tpt170)
REVERT: I   73 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7013 (mtm110)
REVERT: I   77 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7777 (ttmm)
REVERT: J   73 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6854 (mtm180)
REVERT: J  122 LEU cc_start: 0.8598 (mt) cc_final: 0.8377 (tt)
  outliers start: 43
  outliers final: 15
  residues processed: 218
  average time/residue: 0.2918
  time to fit residues: 81.9069
Evaluate side-chains
  203 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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   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  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   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   73 ARG
Chi-restraints excluded: chain I residue   99 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9720  Z= 0.195
  Angle     :  0.622   7.190  13140  Z= 0.339
  Chirality :  0.040   0.214   1390
  Planarity :  0.004   0.028   1690
  Dihedral  :  4.744  15.744   1260
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.54 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 25.70 %
    Favored  : 71.80 %
  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:  1.79 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.05 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 HIS   0.002   0.001   HIS E  54 
 PHE   0.007   0.001   PHE H  64 
 TYR   0.013   0.001   TYR I  72 
 ARG   0.002   0.000   ARG H  36 

*********************** 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
  209 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 1.043 
Fit side-chains
REVERT: B   55 MET cc_start: 0.7010 (mmm) cc_final: 0.6518 (mmp)
REVERT: B   73 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6955 (mtm180)
REVERT: B  122 LEU cc_start: 0.8598 (mt) cc_final: 0.8318 (tt)
REVERT: C  122 LEU cc_start: 0.8630 (mt) cc_final: 0.8306 (tt)
REVERT: D   55 MET cc_start: 0.7309 (mmm) cc_final: 0.7018 (mmp)
REVERT: D   62 ARG cc_start: 0.8736 (tpt170) cc_final: 0.8517 (tpt170)
REVERT: D   77 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7704 (ttmm)
REVERT: G   55 MET cc_start: 0.7216 (mmm) cc_final: 0.6850 (mmp)
REVERT: G  122 LEU cc_start: 0.8591 (mt) cc_final: 0.8317 (tt)
REVERT: H  122 LEU cc_start: 0.8615 (mt) cc_final: 0.8257 (tt)
REVERT: I   55 MET cc_start: 0.7291 (mmm) cc_final: 0.6988 (mmp)
REVERT: I   62 ARG cc_start: 0.8743 (tpt170) cc_final: 0.8455 (tpt170)
REVERT: I   73 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6881 (mtm110)
REVERT: I   77 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7695 (ttmm)
REVERT: J   73 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6836 (mtm180)
  outliers start: 25
  outliers final: 17
  residues processed: 201
  average time/residue: 0.2887
  time to fit residues: 74.9747
Evaluate side-chains
  190 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
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  113 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   73 ARG
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   73 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0370
   chunk 20 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0980
   chunk 83 optimal weight:    8.9990
   chunk 96 optimal weight:    0.7980
   chunk 101 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4161

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= 0.185
  Angle     :  0.641   7.599  13140  Z= 0.348
  Chirality :  0.040   0.198   1390
  Planarity :  0.004   0.029   1690
  Dihedral  :  4.614  15.815   1260
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.10 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.90 %
    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: -0.07 (0.26), residues: 1130
  helix:  1.81 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.96 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP J  43 
 HIS   0.003   0.001   HIS A  20 
 PHE   0.007   0.001   PHE C  64 
 TYR   0.015   0.001   TYR J  72 
 ARG   0.004   0.000   ARG E  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
  212 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   66 MET cc_start: 0.8957 (tmm) cc_final: 0.8525 (tmm)
REVERT: A   73 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6812 (mtp180)
REVERT: B   55 MET cc_start: 0.7164 (mmm) cc_final: 0.6753 (mmp)
REVERT: B   73 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6928 (mtm180)
REVERT: B  101 MET cc_start: 0.8674 (ttm) cc_final: 0.8404 (ttm)
REVERT: C  122 LEU cc_start: 0.8566 (mt) cc_final: 0.8283 (tt)
REVERT: D   55 MET cc_start: 0.7340 (mmm) cc_final: 0.7053 (mmp)
REVERT: F   66 MET cc_start: 0.8954 (tmm) cc_final: 0.8545 (tmm)
REVERT: H  122 LEU cc_start: 0.8530 (mt) cc_final: 0.8307 (tt)
REVERT: I   55 MET cc_start: 0.7290 (mmm) cc_final: 0.7009 (mmp)
REVERT: I   62 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8469 (tpt170)
REVERT: I   73 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6849 (mtm180)
REVERT: J   55 MET cc_start: 0.6646 (mmm) cc_final: 0.6287 (mmp)
REVERT: J   73 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6832 (mtm180)
  outliers start: 26
  outliers final: 17
  residues processed: 207
  average time/residue: 0.2854
  time to fit residues: 76.0937
Evaluate side-chains
  193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
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   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
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  113 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   73 ARG
Chi-restraints excluded: chain I residue   99 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0370
   chunk 43 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 104 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   overall best weight:    1.1262

-------------------------------------------------------------------------------
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**
** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 100 GLN
** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9720  Z= 0.222
  Angle     :  0.664   8.109  13140  Z= 0.357
  Chirality :  0.042   0.233   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.637  16.496   1260
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.57 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 26.40 %
    Favored  : 71.80 %
  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: -0.05 (0.26), residues: 1130
  helix:  1.80 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.87 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  43 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.008   0.001   PHE C  64 
 TYR   0.014   0.002   TYR E  72 
 ARG   0.004   0.000   ARG B  44 

*********************** 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
  197 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 1.140 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6829 (mtm180)
REVERT: B   55 MET cc_start: 0.7081 (mmm) cc_final: 0.6824 (mmp)
REVERT: B   73 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6963 (mtm180)
REVERT: C   55 MET cc_start: 0.7116 (mmm) cc_final: 0.6826 (mmp)
REVERT: C  122 LEU cc_start: 0.8546 (mt) cc_final: 0.8325 (tt)
REVERT: D   55 MET cc_start: 0.7388 (mmm) cc_final: 0.7125 (mmp)
REVERT: D  113 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8318 (tp)
REVERT: F   66 MET cc_start: 0.8988 (tmm) cc_final: 0.8540 (tmm)
REVERT: F   73 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6913 (mtm180)
REVERT: G   55 MET cc_start: 0.6904 (mmm) cc_final: 0.6523 (mmp)
REVERT: H   55 MET cc_start: 0.7120 (mmm) cc_final: 0.6828 (mmp)
REVERT: I   55 MET cc_start: 0.7427 (mmm) cc_final: 0.7160 (mmp)
REVERT: I   62 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8496 (tpt170)
  outliers start: 18
  outliers final: 12
  residues processed: 191
  average time/residue: 0.3013
  time to fit residues: 73.9190
Evaluate side-chains
  190 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
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   37 VAL
Chi-restraints excluded: chain B 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   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
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 49 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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**
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   9720  Z= 0.205
  Angle     :  0.668   8.362  13140  Z= 0.358
  Chirality :  0.041   0.218   1390
  Planarity :  0.004   0.031   1690
  Dihedral  :  4.558  16.672   1260
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 28.00 %
    Favored  : 70.50 %
  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:  1.79 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.80 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  43 
 HIS   0.002   0.000   HIS J  54 
 PHE   0.006   0.001   PHE C  64 
 TYR   0.014   0.001   TYR J  72 
 ARG   0.003   0.000   ARG C  36 

********************** 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
  193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6817 (mtm180)
REVERT: B   55 MET cc_start: 0.7154 (mmm) cc_final: 0.6917 (mmp)
REVERT: B   73 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6970 (mtm180)
REVERT: B  101 MET cc_start: 0.8683 (ttm) cc_final: 0.8419 (ttm)
REVERT: C   47 ARG cc_start: 0.8579 (ttp-170) cc_final: 0.8353 (ttp-170)
REVERT: D   55 MET cc_start: 0.7422 (mmm) cc_final: 0.7163 (mmp)
REVERT: D  113 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8315 (tp)
REVERT: E   55 MET cc_start: 0.6850 (mmm) cc_final: 0.6560 (mmp)
REVERT: F   66 MET cc_start: 0.8950 (tmm) cc_final: 0.8527 (tmm)
REVERT: G   55 MET cc_start: 0.6977 (mmm) cc_final: 0.6612 (mmp)
REVERT: H   47 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8368 (ttp-170)
REVERT: H   55 MET cc_start: 0.7151 (mmm) cc_final: 0.6883 (mmp)
REVERT: I   55 MET cc_start: 0.7419 (mmm) cc_final: 0.7158 (mmp)
REVERT: I   62 ARG cc_start: 0.8720 (tpt170) cc_final: 0.8479 (tpt170)
REVERT: J   55 MET cc_start: 0.6468 (mmm) cc_final: 0.6091 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 188
  average time/residue: 0.3033
  time to fit residues: 73.0177
Evaluate side-chains
  187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
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   37 VAL
Chi-restraints excluded: chain B 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  113 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G 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 80 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 11 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
** 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 = 0.3930 r_free = 0.3930 target = 0.172657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.127834 restraints weight = 10774.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.98
r_work: 0.3293 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9720  Z= 0.207
  Angle     :  0.668   8.470  13140  Z= 0.357
  Chirality :  0.041   0.225   1390
  Planarity :  0.004   0.030   1690
  Dihedral  :  4.503  16.617   1260
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.04 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 28.00 %
    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:  1.79 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.76 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP J  43 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.006   0.001   PHE E  64 
 TYR   0.012   0.001   TYR C  72 
 ARG   0.003   0.000   ARG C  36 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2231.84 seconds
wall clock time: 41 minutes 24.18 seconds (2484.18 seconds total)