Starting phenix.real_space_refine
on Tue Feb 11 11:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ys8_10893/02_2025/6ys8_10893.cif"
  }
  resolution = 3.9
  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=   0.000 sd=   0.002
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      29      5.16       5
     C    3661      2.51       5
     N     882      2.21       5
     O    1052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5624
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1695
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 3, 'TRANS': 214}
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1704
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 3, 'TRANS': 215}
    Chain: "G"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 445
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
    Chain: "F"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 445
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
    Chain: "E"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 445
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
    Chain: "D"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 445
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 445
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
  Time building chain proxies: 3.84, per 1000 atoms: 0.68
  Number of scatterers: 5624
  At special positions: 0
  Unit cell: (70.692, 63.294, 115.902, 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      29     16.00
     O    1052      8.00
     N     882      7.00
     C    3661      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: 1.33
  Conformation dependent library (CDL) restraints added in 647.3 milliseconds
  

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1358

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      72.6% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 23
    Processing helix  chain 'A' and resid 32 through 68
      removed outlier: 4.067A  pdb=" N   SER A  56 " --> pdb=" O   THR A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 101
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.933A  pdb=" N   PHE A 128 " --> pdb=" O   ASP A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 155
    Processing helix  chain 'A' and resid 161 through 172
    Processing helix  chain 'A' and resid 186 through 191
    Processing helix  chain 'A' and resid 196 through 224
    Processing helix  chain 'B' and resid 8 through 29
      removed outlier: 3.906A  pdb=" N   MET B  12 " --> pdb=" O   PRO B   8 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   LEU B  18 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 68
      removed outlier: 3.954A  pdb=" N   LEU B  38 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   THR B  52 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 101
    Processing helix  chain 'B' and resid 124 through 126
      No H-bonds generated for 'chain 'B' and resid 124 through 126'
    Processing helix  chain 'B' and resid 134 through 155
    Processing helix  chain 'B' and resid 161 through 172
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 196 through 225
    Processing helix  chain 'G' and resid 5 through 28
    Processing helix  chain 'G' and resid 38 through 56
    Processing helix  chain 'F' and resid 6 through 30
      removed outlier: 4.020A  pdb=" N   ALA F  12 " --> pdb=" O   VAL F   8 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE F  21 " --> pdb=" O   ALA F  17 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 38 through 56
      removed outlier: 3.633A  pdb=" N   ILE F  52 " --> pdb=" O   THR F  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 5 through 30
      removed outlier: 4.358A  pdb=" N   ALA E  17 " --> pdb=" O   TYR E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 56
    Processing helix  chain 'D' and resid 5 through 28
    Processing helix  chain 'D' and resid 38 through 56
    Processing helix  chain 'C' and resid 8 through 30
    Processing helix  chain 'C' and resid 41 through 56
      removed outlier: 3.776A  pdb=" N   LEU C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 129

    423 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 1.50 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: 1465
        1.34 -     1.45: 998
        1.45 -     1.57: 3199
        1.57 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 5720
  Sorted by residual:
  bond pdb=" N   VAL B  32 "
       pdb=" CA  VAL B  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.10e+01
  bond pdb=" N   GLY C  38 "
       pdb=" CA  GLY C  38 "
    ideal  model  delta    sigma   weight residual
    1.446  1.478 -0.031 1.08e-02 8.57e+03 8.42e+00
  bond pdb=" N   ILE C  33 "
       pdb=" CA  ILE C  33 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.69e+00
  bond pdb=" N   ILE A  13 "
       pdb=" CA  ILE A  13 "
    ideal  model  delta    sigma   weight residual
    1.463  1.494 -0.031 1.14e-02 7.69e+03 7.41e+00
  bond pdb=" N   ILE B  33 "
       pdb=" CA  ILE B  33 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.030 1.17e-02 7.31e+03 6.79e+00
  ... (remaining 5715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.87: 7662
        4.87 -     9.75: 36
        9.75 -    14.62: 1
       14.62 -    19.50: 0
       19.50 -    24.37: 1
  Bond angle restraints: 7700
  Sorted by residual:
  angle pdb=" C   ILE C  33 "
        pdb=" CA  ILE C  33 "
        pdb=" CB  ILE C  33 "
      ideal   model   delta    sigma   weight residual
     111.29  135.66  -24.37 1.64e+00 3.72e-01 2.21e+02
  angle pdb=" N   VAL C  40 "
        pdb=" CA  VAL C  40 "
        pdb=" C   VAL C  40 "
      ideal   model   delta    sigma   weight residual
     111.62  105.82    5.80 7.90e-01 1.60e+00 5.40e+01
  angle pdb=" C   LYS B  30 "
        pdb=" CA  LYS B  30 "
        pdb=" CB  LYS B  30 "
      ideal   model   delta    sigma   weight residual
     116.54  110.28    6.26 1.15e+00 7.56e-01 2.96e+01
  angle pdb=" C   GLU A  31 "
        pdb=" N   VAL A  32 "
        pdb=" CA  VAL A  32 "
      ideal   model   delta    sigma   weight residual
     121.97  130.50   -8.53 1.80e+00 3.09e-01 2.25e+01
  angle pdb=" N   VAL A  32 "
        pdb=" CA  VAL A  32 "
        pdb=" C   VAL A  32 "
      ideal   model   delta    sigma   weight residual
     109.34  119.12   -9.78 2.08e+00 2.31e-01 2.21e+01
  ... (remaining 7695 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 3008
       17.71 -    35.43: 323
       35.43 -    53.14: 73
       53.14 -    70.86: 13
       70.86 -    88.57: 6
  Dihedral angle restraints: 3423
    sinusoidal: 1310
      harmonic: 2113
  Sorted by residual:
  dihedral pdb=" C   ILE C  33 "
           pdb=" N   ILE C  33 "
           pdb=" CA  ILE C  33 "
           pdb=" CB  ILE C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -166.17   44.17     0      2.50e+00 1.60e-01 3.12e+02
  dihedral pdb=" N   ILE C  33 "
           pdb=" C   ILE C  33 "
           pdb=" CA  ILE C  33 "
           pdb=" CB  ILE C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  161.38  -37.98     0      2.50e+00 1.60e-01 2.31e+02
  dihedral pdb=" CD  ARG A   9 "
           pdb=" NE  ARG A   9 "
           pdb=" CZ  ARG A   9 "
           pdb=" NH1 ARG A   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.57  -88.57     1      1.00e+01 1.00e-02 9.36e+01
  ... (remaining 3420 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.340: 898
       0.340 -    0.680: 0
       0.680 -    1.020: 0
       1.020 -    1.359: 0
       1.359 -    1.699: 1
  Chirality restraints: 899
  Sorted by residual:
  chirality pdb=" CA  ILE C  33 "
            pdb=" N   ILE C  33 "
            pdb=" C   ILE C  33 "
            pdb=" CB  ILE C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    0.73    1.70 2.00e-01 2.50e+01 7.22e+01
  chirality pdb=" CB  VAL F   8 "
            pdb=" CA  VAL F   8 "
            pdb=" CG1 VAL F   8 "
            pdb=" CG2 VAL F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  VAL B  32 "
            pdb=" CA  VAL B  32 "
            pdb=" CG1 VAL B  32 "
            pdb=" CG2 VAL B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 896 not shown)

  Planarity restraints: 952
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A   9 "   -1.098 9.50e-02 1.11e+02   4.92e-01 1.46e+02
        pdb=" NE  ARG A   9 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A   9 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A   9 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A   9 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B   9 "   -0.526 9.50e-02 1.11e+02   2.36e-01 3.40e+01
        pdb=" NE  ARG B   9 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B   9 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B   9 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  51 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.72e+00
        pdb=" C   VAL B  51 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   VAL B  51 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR B  52 "    0.013 2.00e-02 2.50e+03
  ... (remaining 949 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 8
        2.20 -     2.87: 2117
        2.87 -     3.55: 8427
        3.55 -     4.22: 12386
        4.22 -     4.90: 21774
  Nonbonded interactions: 44712
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B   9 "
            pdb=" OE2 GLU C  49 "
     model   vdw
     1.522 3.120
  nonbonded pdb=" OE1 GLN A  10 "
            pdb=" NE2 GLN B  10 "
     model   vdw
     1.691 3.120
  nonbonded pdb=" CE  MET A  12 "
            pdb=" OE1 GLU E  49 "
     model   vdw
     1.804 3.460
  nonbonded pdb=" CZ  ARG B   9 "
            pdb=" OE2 GLU C  49 "
     model   vdw
     1.880 3.270
  nonbonded pdb=" NH1 ARG B   9 "
            pdb=" OE2 GLU C  49 "
     model   vdw
     1.925 3.120
  ... (remaining 44707 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' and resid 7 through 224)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.230
  Find NCS groups from input model:        0.190
  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:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5720  Z= 0.393
  Angle     :  1.035  24.371   7700  Z= 0.619
  Chirality :  0.080   1.699    899
  Planarity :  0.019   0.492    952
  Dihedral  : 15.755  88.569   2065
  Min Nonbonded Distance : 1.522

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  2.21 %
    Allowed  :  6.36 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.67 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.23), residues: 723
  helix: -1.92 (0.17), residues: 510
  sheet:  None (None), residues: 0
  loop : -3.73 (0.33), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 127 
 HIS   0.004   0.001   HIS B  80 
 PHE   0.021   0.002   PHE A  20 
 TYR   0.017   0.002   TYR A  92 
 ARG   0.001   0.000   ARG B   9 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 242
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: A   74 LYS cc_start: 0.8950 (tptt) cc_final: 0.8590 (tmmt)
REVERT: A   83 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7914 (tp40)
REVERT: A  145 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8298 (mm-30)
REVERT: A  146 LYS cc_start: 0.8648 (tttm) cc_final: 0.8371 (ttpt)
REVERT: A  180 LYS cc_start: 0.8471 (pttt) cc_final: 0.8198 (mtmt)
REVERT: A  219 TYR cc_start: 0.8834 (m-10) cc_final: 0.8604 (m-80)
REVERT: A  220 ASN cc_start: 0.8721 (m110) cc_final: 0.8509 (m110)
REVERT: B   27 ASN cc_start: 0.9271 (t0) cc_final: 0.9060 (t0)
REVERT: B   99 GLN cc_start: 0.8702 (tt0) cc_final: 0.8034 (tp40)
REVERT: B  123 ASN cc_start: 0.8828 (p0) cc_final: 0.8203 (p0)
REVERT: G    7 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8238 (tmtt)
REVERT: F    9 MET cc_start: 0.8878 (tpp) cc_final: 0.8349 (tpp)
REVERT: F   32 GLU cc_start: 0.8649 (pm20) cc_final: 0.8319 (pm20)
REVERT: E   55 LEU cc_start: 0.8974 (pp) cc_final: 0.8710 (mt)
REVERT: D    7 LYS cc_start: 0.9280 (mttt) cc_final: 0.8320 (tmtt)
REVERT: C   22 VAL cc_start: 0.9571 (p) cc_final: 0.9286 (p)
  outliers start: 10
  outliers final: 6
  residues processed: 248
  average time/residue: 0.1656
  time to fit residues: 53.3783
Evaluate side-chains
  217 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 211
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ARG
Chi-restraints excluded: chain A residue   11 LYS
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain C residue   31 PHE
Chi-restraints excluded: chain C residue   36 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
A 220 ASN
B  54 ASN
C  30 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.106181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.085226 restraints weight = 11923.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087938 restraints weight = 7801.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.088922 restraints weight = 5731.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5720  Z= 0.209
  Angle     :  0.704   9.014   7700  Z= 0.372
  Chirality :  0.042   0.176    899
  Planarity :  0.004   0.032    952
  Dihedral  :  6.391  54.536    776
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.70 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.18 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.32 (0.29), residues: 723
  helix: -0.01 (0.21), residues: 523
  sheet:  None (None), residues: 0
  loop : -3.13 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 127 
 HIS   0.001   0.001   HIS G  30 
 PHE   0.025   0.002   PHE D  31 
 TYR   0.015   0.002   TYR B 147 
 ARG   0.003   0.001   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 229
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.7381 (ttp) cc_final: 0.5811 (tpp)
REVERT: A   31 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8142 (pt0)
REVERT: A   74 LYS cc_start: 0.8910 (tptt) cc_final: 0.8585 (tmmt)
REVERT: A   83 GLN cc_start: 0.8566 (tm-30) cc_final: 0.7805 (tp40)
REVERT: A  145 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: A  146 LYS cc_start: 0.8613 (tttm) cc_final: 0.8290 (ttpt)
REVERT: A  220 ASN cc_start: 0.8646 (m-40) cc_final: 0.8411 (m110)
REVERT: B   16 MET cc_start: 0.9397 (mmm) cc_final: 0.9165 (mmp)
REVERT: B   99 GLN cc_start: 0.8628 (tt0) cc_final: 0.7632 (tm-30)
REVERT: B  123 ASN cc_start: 0.8777 (p0) cc_final: 0.7562 (p0)
REVERT: B  124 ILE cc_start: 0.8356 (pt) cc_final: 0.8086 (pt)
REVERT: G    7 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8549 (tttt)
REVERT: G   49 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7851 (mm-30)
REVERT: F    4 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8078 (pp)
REVERT: F    9 MET cc_start: 0.8750 (tpp) cc_final: 0.8486 (tpp)
REVERT: D    4 LEU cc_start: 0.7121 (mm) cc_final: 0.6893 (mt)
REVERT: D    7 LYS cc_start: 0.9412 (mttt) cc_final: 0.8538 (tmtt)
REVERT: D    9 MET cc_start: 0.7971 (tpp) cc_final: 0.7662 (mmp)
REVERT: D   32 GLU cc_start: 0.8070 (pm20) cc_final: 0.7767 (mp0)
REVERT: C    9 MET cc_start: 0.8074 (mmm) cc_final: 0.7820 (mpp)
REVERT: C   15 MET cc_start: 0.8436 (mmm) cc_final: 0.7972 (tpp)
REVERT: C   31 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7761 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 236
  average time/residue: 0.1464
  time to fit residues: 46.1698
Evaluate side-chains
  221 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 208
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  138 ASN
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   31 PHE
Chi-restraints excluded: chain C residue   36 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   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 138 ASN
B  47 ASN
** B  54 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.107133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.085648 restraints weight = 12314.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.088531 restraints weight = 7924.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.089473 restraints weight = 5722.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5720  Z= 0.207
  Angle     :  0.701   9.752   7700  Z= 0.365
  Chirality :  0.042   0.183    899
  Planarity :  0.004   0.026    952
  Dihedral  :  5.768  53.150    765
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.70 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.88 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.22 (0.31), residues: 723
  helix:  0.83 (0.22), residues: 521
  sheet:  None (None), residues: 0
  loop : -2.76 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 127 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.017   0.001   PHE E  11 
 TYR   0.019   0.002   TYR B 147 
 ARG   0.001   0.000   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.7210 (OUTLIER) cc_final: 0.6916 (p)
REVERT: A   31 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7914 (pt0)
REVERT: A   74 LYS cc_start: 0.8910 (tptt) cc_final: 0.8580 (tmmt)
REVERT: A   81 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8841 (mptt)
REVERT: A   83 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: A   92 TYR cc_start: 0.8987 (t80) cc_final: 0.8601 (t80)
REVERT: A  145 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8365 (mm-30)
REVERT: A  217 ASP cc_start: 0.9067 (p0) cc_final: 0.8812 (p0)
REVERT: A  220 ASN cc_start: 0.8678 (m-40) cc_final: 0.8402 (m110)
REVERT: B   16 MET cc_start: 0.9337 (mmm) cc_final: 0.9128 (mmp)
REVERT: B   26 MET cc_start: 0.8246 (mtp) cc_final: 0.7786 (mtm)
REVERT: B  123 ASN cc_start: 0.8733 (p0) cc_final: 0.8487 (p0)
REVERT: G    7 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8541 (tttt)
REVERT: G   39 THR cc_start: 0.9048 (m) cc_final: 0.8792 (p)
REVERT: G   49 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8460 (mm-30)
REVERT: F    4 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8186 (pp)
REVERT: F    9 MET cc_start: 0.8741 (tpp) cc_final: 0.8494 (tpp)
REVERT: E    6 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8431 (mmmt)
REVERT: E    9 MET cc_start: 0.8465 (ppp) cc_final: 0.8178 (ppp)
REVERT: D    4 LEU cc_start: 0.7157 (mm) cc_final: 0.6917 (mt)
REVERT: D    7 LYS cc_start: 0.9407 (mttt) cc_final: 0.8525 (tmtt)
REVERT: D    9 MET cc_start: 0.8076 (tpp) cc_final: 0.7778 (mmp)
REVERT: C    9 MET cc_start: 0.8133 (mmm) cc_final: 0.7919 (mpp)
REVERT: C   15 MET cc_start: 0.8516 (mmm) cc_final: 0.8022 (tpp)
REVERT: C   31 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7598 (m-80)
  outliers start: 28
  outliers final: 17
  residues processed: 232
  average time/residue: 0.1527
  time to fit residues: 46.9957
Evaluate side-chains
  218 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain C residue   31 PHE
Chi-restraints excluded: chain C residue   36 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 11 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 19 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
B  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.108302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.087442 restraints weight = 12509.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.090420 restraints weight = 7977.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.091559 restraints weight = 5641.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5720  Z= 0.188
  Angle     :  0.708  11.004   7700  Z= 0.358
  Chirality :  0.042   0.220    899
  Planarity :  0.003   0.024    952
  Dihedral  :  5.573  55.735    765
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.43 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 23.81 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.12 (0.32), residues: 723
  helix:  1.04 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -2.59 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 207 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.014   0.001   PHE E  11 
 TYR   0.028   0.002   TYR A 219 
 ARG   0.001   0.000   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 221
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6944 (OUTLIER) cc_final: 0.6637 (p)
REVERT: A   31 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7833 (pt0)
REVERT: A   74 LYS cc_start: 0.8878 (tptt) cc_final: 0.8564 (tmmt)
REVERT: A   77 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: A   81 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8774 (mptt)
REVERT: A   83 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: A   92 TYR cc_start: 0.8960 (t80) cc_final: 0.8618 (t80)
REVERT: A  145 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8450 (mm-30)
REVERT: A  146 LYS cc_start: 0.8531 (tttm) cc_final: 0.8263 (mtmt)
REVERT: A  217 ASP cc_start: 0.9067 (p0) cc_final: 0.8786 (p0)
REVERT: A  220 ASN cc_start: 0.8706 (m-40) cc_final: 0.8444 (m110)
REVERT: B   12 MET cc_start: 0.8853 (tmm) cc_final: 0.8615 (tmm)
REVERT: B   26 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (mtm)
REVERT: G    7 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8512 (tttt)
REVERT: G   39 THR cc_start: 0.8966 (m) cc_final: 0.8584 (p)
REVERT: G   49 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8525 (mm-30)
REVERT: F    4 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8208 (pp)
REVERT: F    9 MET cc_start: 0.8788 (tpp) cc_final: 0.8510 (tpp)
REVERT: F   30 HIS cc_start: 0.8257 (m90) cc_final: 0.7993 (m170)
REVERT: E    6 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8439 (mmmt)
REVERT: E    9 MET cc_start: 0.8485 (ppp) cc_final: 0.8237 (ppp)
REVERT: E   53 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8302 (m-80)
REVERT: D    7 LYS cc_start: 0.9397 (mttt) cc_final: 0.8517 (tmtt)
REVERT: D    9 MET cc_start: 0.8120 (tpp) cc_final: 0.7913 (mmp)
REVERT: C    9 MET cc_start: 0.8241 (mmm) cc_final: 0.8022 (mpp)
REVERT: C   15 MET cc_start: 0.8501 (mmm) cc_final: 0.8076 (mmm)
  outliers start: 27
  outliers final: 16
  residues processed: 233
  average time/residue: 0.1468
  time to fit residues: 45.8120
Evaluate side-chains
  224 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   36 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.110459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.088413 restraints weight = 12644.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091476 restraints weight = 8374.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.092061 restraints weight = 6342.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5720  Z= 0.188
  Angle     :  0.713   9.754   7700  Z= 0.360
  Chirality :  0.042   0.222    899
  Planarity :  0.003   0.024    952
  Dihedral  :  5.099  57.689    763
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 25.85 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.37 (0.32), residues: 723
  helix:  1.16 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.53 (0.47), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 207 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.022   0.001   PHE G  31 
 TYR   0.039   0.002   TYR A 219 
 ARG   0.001   0.000   ARG A   9 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 212
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6648 (OUTLIER) cc_final: 0.6405 (p)
REVERT: A   31 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7838 (pt0)
REVERT: A   74 LYS cc_start: 0.8860 (tptt) cc_final: 0.8570 (tmmt)
REVERT: A   77 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: A   81 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8775 (mptt)
REVERT: A   83 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: A   91 ASP cc_start: 0.7893 (m-30) cc_final: 0.7655 (m-30)
REVERT: A   92 TYR cc_start: 0.8915 (t80) cc_final: 0.8607 (t80)
REVERT: A  145 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8489 (mm-30)
REVERT: A  146 LYS cc_start: 0.8513 (tttm) cc_final: 0.8285 (mtpt)
REVERT: A  180 LYS cc_start: 0.8593 (mtmt) cc_final: 0.7701 (mtmt)
REVERT: A  217 ASP cc_start: 0.9039 (p0) cc_final: 0.8737 (p0)
REVERT: A  220 ASN cc_start: 0.8691 (m-40) cc_final: 0.8401 (m110)
REVERT: B   26 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7713 (mtm)
REVERT: B   99 GLN cc_start: 0.8741 (tt0) cc_final: 0.7896 (tm-30)
REVERT: B  116 GLU cc_start: 0.7453 (pt0) cc_final: 0.6382 (pt0)
REVERT: G    7 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8497 (tttt)
REVERT: F    4 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8252 (pp)
REVERT: F    9 MET cc_start: 0.8759 (tpp) cc_final: 0.8479 (tpp)
REVERT: E    6 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8542 (mmmt)
REVERT: E    9 MET cc_start: 0.8499 (ppp) cc_final: 0.8237 (ppp)
REVERT: E   53 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8241 (m-10)
REVERT: D    7 LYS cc_start: 0.9394 (mttt) cc_final: 0.8546 (tmtt)
REVERT: D    9 MET cc_start: 0.8122 (tpp) cc_final: 0.7817 (mmp)
REVERT: C   15 MET cc_start: 0.8403 (mmm) cc_final: 0.7981 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 225
  average time/residue: 0.1394
  time to fit residues: 41.8504
Evaluate side-chains
  230 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.088686 restraints weight = 12410.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.091561 restraints weight = 8869.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092779 restraints weight = 6510.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5720  Z= 0.199
  Angle     :  0.751  11.239   7700  Z= 0.377
  Chirality :  0.044   0.233    899
  Planarity :  0.003   0.023    952
  Dihedral  :  4.978  59.345    761
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.84 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 28.40 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.47 (0.32), residues: 723
  helix:  1.19 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -2.39 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 207 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.020   0.001   PHE G  31 
 TYR   0.044   0.002   TYR A 219 
 ARG   0.001   0.000   ARG A   9 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6444 (OUTLIER) cc_final: 0.6132 (p)
REVERT: A   31 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7810 (pt0)
REVERT: A   74 LYS cc_start: 0.8846 (tptt) cc_final: 0.8583 (tmmt)
REVERT: A   77 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7586 (mm-30)
REVERT: A   81 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8886 (mptt)
REVERT: A   83 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: A   91 ASP cc_start: 0.7857 (m-30) cc_final: 0.7630 (m-30)
REVERT: A   92 TYR cc_start: 0.8905 (t80) cc_final: 0.8629 (t80)
REVERT: A  145 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8543 (mm-30)
REVERT: A  146 LYS cc_start: 0.8487 (tttm) cc_final: 0.8242 (mtpt)
REVERT: A  180 LYS cc_start: 0.8625 (mtmt) cc_final: 0.7749 (mtmt)
REVERT: A  217 ASP cc_start: 0.8991 (p0) cc_final: 0.8670 (p0)
REVERT: A  220 ASN cc_start: 0.8652 (m-40) cc_final: 0.8369 (m110)
REVERT: B   26 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7671 (mtm)
REVERT: B   99 GLN cc_start: 0.8762 (tt0) cc_final: 0.7907 (tm-30)
REVERT: B  116 GLU cc_start: 0.7419 (pt0) cc_final: 0.6354 (pt0)
REVERT: G    7 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8439 (tttt)
REVERT: F    4 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8277 (pp)
REVERT: F    9 MET cc_start: 0.8643 (tpp) cc_final: 0.8392 (tpp)
REVERT: E    6 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8530 (mmmt)
REVERT: E    9 MET cc_start: 0.8464 (ppp) cc_final: 0.8208 (ppp)
REVERT: E   49 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8128 (mm-30)
REVERT: E   53 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8185 (m-10)
REVERT: D    7 LYS cc_start: 0.9402 (mttt) cc_final: 0.8570 (tmtt)
REVERT: D    9 MET cc_start: 0.8084 (tpp) cc_final: 0.7742 (mmp)
REVERT: C   15 MET cc_start: 0.8411 (mmm) cc_final: 0.8006 (mmm)
  outliers start: 25
  outliers final: 19
  residues processed: 221
  average time/residue: 0.1516
  time to fit residues: 44.5303
Evaluate side-chains
  227 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.0670
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** 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 = 0.3604 r_free = 0.3604 target = 0.111938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.089906 restraints weight = 12680.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.092841 restraints weight = 9023.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.093605 restraints weight = 6765.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5720  Z= 0.190
  Angle     :  0.758  11.225   7700  Z= 0.376
  Chirality :  0.045   0.297    899
  Planarity :  0.003   0.023    952
  Dihedral  :  4.908  58.211    761
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.55 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.64 (0.32), residues: 723
  helix:  1.36 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -2.27 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 127 
 HIS   0.002   0.001   HIS C  30 
 PHE   0.019   0.001   PHE G  31 
 TYR   0.017   0.002   TYR A  17 
 ARG   0.002   0.000   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 211
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.8212 (tpp) cc_final: 0.7963 (tpp)
REVERT: A   29 SER cc_start: 0.6053 (OUTLIER) cc_final: 0.5768 (p)
REVERT: A   31 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7771 (pt0)
REVERT: A   74 LYS cc_start: 0.8843 (tptt) cc_final: 0.8587 (tmmt)
REVERT: A   77 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7594 (mm-30)
REVERT: A   81 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8894 (mptt)
REVERT: A   91 ASP cc_start: 0.7798 (m-30) cc_final: 0.7564 (m-30)
REVERT: A   92 TYR cc_start: 0.8882 (t80) cc_final: 0.8646 (t80)
REVERT: A  145 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8533 (mm-30)
REVERT: A  146 LYS cc_start: 0.8483 (tttm) cc_final: 0.8259 (mtpt)
REVERT: A  180 LYS cc_start: 0.8624 (mtmt) cc_final: 0.7966 (mtmt)
REVERT: A  217 ASP cc_start: 0.9014 (p0) cc_final: 0.8658 (p0)
REVERT: A  220 ASN cc_start: 0.8638 (m-40) cc_final: 0.8304 (m110)
REVERT: B   26 MET cc_start: 0.8030 (mtp) cc_final: 0.7601 (mtm)
REVERT: B   99 GLN cc_start: 0.8716 (tt0) cc_final: 0.7871 (tm-30)
REVERT: G    7 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8364 (ttpt)
REVERT: G   49 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: F    4 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (pp)
REVERT: F    9 MET cc_start: 0.8647 (tpp) cc_final: 0.8374 (tpp)
REVERT: E    6 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8558 (mmmt)
REVERT: E    9 MET cc_start: 0.8499 (ppp) cc_final: 0.8244 (ppp)
REVERT: E   53 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8122 (m-80)
REVERT: D    7 LYS cc_start: 0.9384 (mttt) cc_final: 0.8555 (tmtt)
REVERT: D    9 MET cc_start: 0.8140 (tpp) cc_final: 0.7752 (mmp)
REVERT: C   15 MET cc_start: 0.8302 (mmm) cc_final: 0.7912 (mmm)
  outliers start: 24
  outliers final: 17
  residues processed: 222
  average time/residue: 0.1538
  time to fit residues: 45.0231
Evaluate side-chains
  222 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0060
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** 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 = 0.3605 r_free = 0.3605 target = 0.111799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.089653 restraints weight = 12440.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.092730 restraints weight = 8989.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.093771 restraints weight = 6536.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5720  Z= 0.211
  Angle     :  0.794  14.696   7700  Z= 0.392
  Chirality :  0.046   0.356    899
  Planarity :  0.004   0.066    952
  Dihedral  :  4.809  54.473    761
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.91 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.69 (0.32), residues: 723
  helix:  1.33 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.18 (0.48), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 127 
 HIS   0.002   0.001   HIS C  30 
 PHE   0.020   0.001   PHE C  11 
 TYR   0.018   0.001   TYR A  17 
 ARG   0.006   0.001   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6064 (OUTLIER) cc_final: 0.5797 (p)
REVERT: A   31 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7919 (pt0)
REVERT: A   74 LYS cc_start: 0.8856 (tptt) cc_final: 0.8603 (tmmt)
REVERT: A   77 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7611 (mm-30)
REVERT: A   81 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8879 (mptt)
REVERT: A   91 ASP cc_start: 0.7774 (m-30) cc_final: 0.7541 (m-30)
REVERT: A   92 TYR cc_start: 0.8848 (t80) cc_final: 0.8610 (t80)
REVERT: A  145 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: A  146 LYS cc_start: 0.8462 (tttm) cc_final: 0.8221 (mtpt)
REVERT: A  180 LYS cc_start: 0.8631 (mtmt) cc_final: 0.7853 (mtmt)
REVERT: A  217 ASP cc_start: 0.9030 (p0) cc_final: 0.8640 (p0)
REVERT: A  220 ASN cc_start: 0.8622 (m-40) cc_final: 0.8305 (m110)
REVERT: B   26 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7656 (mtm)
REVERT: B   99 GLN cc_start: 0.8718 (tt0) cc_final: 0.8076 (tm-30)
REVERT: G    7 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8372 (ttpt)
REVERT: G   49 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8292 (mm-30)
REVERT: F    4 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8294 (pp)
REVERT: F    9 MET cc_start: 0.8648 (tpp) cc_final: 0.8391 (tpp)
REVERT: E    6 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8562 (mmmt)
REVERT: E    9 MET cc_start: 0.8497 (ppp) cc_final: 0.8260 (ppp)
REVERT: E   53 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8134 (m-80)
REVERT: D    7 LYS cc_start: 0.9395 (mttt) cc_final: 0.8568 (tmtt)
REVERT: D    9 MET cc_start: 0.8103 (tpp) cc_final: 0.7698 (mmp)
REVERT: C   15 MET cc_start: 0.8266 (mmm) cc_final: 0.7875 (mmm)
  outliers start: 28
  outliers final: 19
  residues processed: 221
  average time/residue: 0.1492
  time to fit residues: 43.9371
Evaluate side-chains
  231 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 207
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0970
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0770
   chunk 63 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.1540

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** 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 = 0.3572 r_free = 0.3572 target = 0.109722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.088228 restraints weight = 12489.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.091276 restraints weight = 8874.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092113 restraints weight = 6474.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5720  Z= 0.238
  Angle     :  0.806  14.531   7700  Z= 0.398
  Chirality :  0.046   0.344    899
  Planarity :  0.004   0.058    952
  Dihedral  :  4.827  53.091    761
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 29.08 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.72 (0.32), residues: 723
  helix:  1.37 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -2.25 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 127 
 HIS   0.002   0.001   HIS C  30 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.017   0.001   TYR D  13 
 ARG   0.002   0.000   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6314 (OUTLIER) cc_final: 0.6027 (p)
REVERT: A   31 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7944 (pt0)
REVERT: A   74 LYS cc_start: 0.8861 (tptt) cc_final: 0.8616 (tmmt)
REVERT: A   77 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A   91 ASP cc_start: 0.7862 (m-30) cc_final: 0.7627 (m-30)
REVERT: A   92 TYR cc_start: 0.8889 (t80) cc_final: 0.8658 (t80)
REVERT: A  145 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8576 (mm-30)
REVERT: A  146 LYS cc_start: 0.8471 (tttm) cc_final: 0.8167 (mtmt)
REVERT: A  180 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8025 (mtmt)
REVERT: A  217 ASP cc_start: 0.9040 (p0) cc_final: 0.8659 (p0)
REVERT: A  220 ASN cc_start: 0.8661 (m-40) cc_final: 0.8333 (m110)
REVERT: B   26 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7676 (mtm)
REVERT: B   99 GLN cc_start: 0.8739 (tt0) cc_final: 0.8166 (tm-30)
REVERT: B  123 ASN cc_start: 0.8896 (p0) cc_final: 0.8677 (p0)
REVERT: G    7 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8437 (tttt)
REVERT: G   49 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8266 (mm-30)
REVERT: F   30 HIS cc_start: 0.8130 (m90) cc_final: 0.7819 (m170)
REVERT: E    6 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8564 (mmmt)
REVERT: E    9 MET cc_start: 0.8486 (ppp) cc_final: 0.8249 (ppp)
REVERT: E   53 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8120 (m-80)
REVERT: D    7 LYS cc_start: 0.9416 (mttt) cc_final: 0.8591 (tmtt)
REVERT: D    9 MET cc_start: 0.8125 (tpp) cc_final: 0.7651 (mmp)
REVERT: C   15 MET cc_start: 0.8285 (mmm) cc_final: 0.7751 (mmm)
  outliers start: 28
  outliers final: 21
  residues processed: 217
  average time/residue: 0.1448
  time to fit residues: 42.0300
Evaluate side-chains
  227 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   41 MET
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 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 = 0.3611 r_free = 0.3611 target = 0.112149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090475 restraints weight = 12621.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.093518 restraints weight = 9166.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.094507 restraints weight = 6709.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5720  Z= 0.215
  Angle     :  0.850  13.913   7700  Z= 0.415
  Chirality :  0.047   0.323    899
  Planarity :  0.004   0.054    952
  Dihedral  :  4.807  51.142    761
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.70 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 29.25 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.80 (0.32), residues: 723
  helix:  1.44 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -2.13 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 127 
 HIS   0.003   0.001   HIS A  80 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.014   0.001   TYR A 147 
 ARG   0.002   0.000   ARG B 120 

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.5996 (OUTLIER) cc_final: 0.5723 (p)
REVERT: A   31 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7952 (pt0)
REVERT: A   74 LYS cc_start: 0.8880 (tptt) cc_final: 0.8621 (tmmt)
REVERT: A   91 ASP cc_start: 0.7826 (m-30) cc_final: 0.7582 (m-30)
REVERT: A   92 TYR cc_start: 0.8849 (t80) cc_final: 0.8620 (t80)
REVERT: A  105 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8149 (pm20)
REVERT: A  145 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8580 (mm-30)
REVERT: A  146 LYS cc_start: 0.8427 (tttm) cc_final: 0.8159 (mtmt)
REVERT: A  180 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8003 (mtmt)
REVERT: A  217 ASP cc_start: 0.9053 (p0) cc_final: 0.8763 (p0)
REVERT: A  220 ASN cc_start: 0.8648 (m-40) cc_final: 0.8324 (m110)
REVERT: B   26 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7643 (mtm)
REVERT: B   96 LEU cc_start: 0.9132 (mt) cc_final: 0.8716 (mp)
REVERT: B   99 GLN cc_start: 0.8735 (tt0) cc_final: 0.8146 (tm-30)
REVERT: G    7 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8418 (tttt)
REVERT: G   49 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8305 (mm-30)
REVERT: F    4 LEU cc_start: 0.8641 (pp) cc_final: 0.8387 (pp)
REVERT: F    9 MET cc_start: 0.8719 (tpp) cc_final: 0.8479 (tpp)
REVERT: F   30 HIS cc_start: 0.8141 (m90) cc_final: 0.7891 (m170)
REVERT: E    6 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8549 (mmmt)
REVERT: E    9 MET cc_start: 0.8509 (ppp) cc_final: 0.8246 (ppp)
REVERT: E   53 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8140 (m-80)
REVERT: D    7 LYS cc_start: 0.9408 (mttt) cc_final: 0.8584 (tmtt)
REVERT: D    9 MET cc_start: 0.8116 (tpp) cc_final: 0.7707 (mmp)
REVERT: C   15 MET cc_start: 0.8332 (mmm) cc_final: 0.7911 (tpp)
  outliers start: 26
  outliers final: 18
  residues processed: 221
  average time/residue: 0.1448
  time to fit residues: 42.9210
Evaluate side-chains
  227 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 SER
Chi-restraints excluded: chain A residue   31 GLU
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0270
   chunk 55 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.1442

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** 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 = 0.3574 r_free = 0.3574 target = 0.109714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.089041 restraints weight = 12713.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.091982 restraints weight = 8633.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.092932 restraints weight = 6235.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5720  Z= 0.255
  Angle     :  0.870  15.158   7700  Z= 0.433
  Chirality :  0.048   0.353    899
  Planarity :  0.004   0.054    952
  Dihedral  :  4.848  50.395    761
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.44 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.80 (0.32), residues: 723
  helix:  1.43 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -2.18 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 127 
 HIS   0.002   0.001   HIS B  80 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.014   0.001   TYR A 147 
 ARG   0.002   0.000   ARG B 120 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1861.32 seconds
wall clock time: 34 minutes 17.42 seconds (2057.42 seconds total)