Starting phenix.real_space_refine
on Thu Mar  6 08:18:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ys8_10893/03_2025/6ys8_10893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ys8_10893/03_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_10893/03_2025/6ys8_10893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2025/6ys8_10893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2025/6ys8_10893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_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-5624/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: 3.89, per 1000 atoms: 0.69
  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: 1.37
  Conformation dependent library (CDL) restraints added in 693.9 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: 0.48
  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: 1.41

  Time building geometry restraints manager: 1.64 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.880
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.460
-------------------------------------------------------------------------------
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  : 0.732 
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: 0.1638
  time to fit residues: 52.9586
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  : 0.592 
-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.106176 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 = 11924.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087928 restraints weight = 7801.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.088920 restraints weight = 5733.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2069

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   9.008   7700  Z= 0.372
  Chirality :  0.042   0.175    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: -1.33 (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  : 0.685 
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: 0.5812 (tpp)
REVERT: A   31 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8142 (pt0)
REVERT: A   74 LYS cc_start: 0.8911 (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: 0.8305 (mm-30)
REVERT: A  146 LYS cc_start: 0.8614 (tttm) cc_final: 0.8290 (ttpt)
REVERT: A  220 ASN cc_start: 0.8646 (m-40) cc_final: 0.8412 (m110)
REVERT: B   16 MET cc_start: 0.9396 (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: 0.7560 (p0)
REVERT: B  124 ILE cc_start: 0.8357 (pt) cc_final: 0.8085 (pt)
REVERT: G    7 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8549 (tttt)
REVERT: G   49 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7854 (mm-30)
REVERT: F    4 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8079 (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: 0.7970 (tpp) cc_final: 0.7663 (mmp)
REVERT: D   32 GLU cc_start: 0.8071 (pm20) cc_final: 0.7767 (mp0)
REVERT: C    9 MET cc_start: 0.8075 (mmm) cc_final: 0.7821 (mpp)
REVERT: C   15 MET cc_start: 0.8437 (mmm) cc_final: 0.7971 (tpp)
REVERT: C   31 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7764 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 236
  average time/residue: 0.1436
  time to fit residues: 45.2081
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  : 0.678 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0782

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.106136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084658 restraints weight = 12369.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.087398 restraints weight = 7920.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.088525 restraints weight = 5801.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5720  Z= 0.221
  Angle     :  0.702   9.748   7700  Z= 0.367
  Chirality :  0.043   0.177    899
  Planarity :  0.004   0.026    952
  Dihedral  :  5.767  53.391    765
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.84 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 19.05 %
    Favored  : 76.02 %
  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:  0.80 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.74 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 127 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.019   0.001   PHE D  26 
 TYR   0.021   0.002   TYR A 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
  246 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 217
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.7321 (OUTLIER) cc_final: 0.7025 (p)
REVERT: A   31 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7964 (pt0)
REVERT: A   74 LYS cc_start: 0.8912 (tptt) cc_final: 0.8585 (tmmt)
REVERT: A   81 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8847 (mptt)
REVERT: A   83 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: A   92 TYR cc_start: 0.9005 (t80) cc_final: 0.8625 (t80)
REVERT: A  145 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8375 (mm-30)
REVERT: A  217 ASP cc_start: 0.9065 (p0) cc_final: 0.8814 (p0)
REVERT: A  220 ASN cc_start: 0.8692 (m-40) cc_final: 0.8436 (m110)
REVERT: B   16 MET cc_start: 0.9342 (mmm) cc_final: 0.9133 (mmp)
REVERT: B   26 MET cc_start: 0.8241 (mtp) cc_final: 0.7772 (mtm)
REVERT: B  123 ASN cc_start: 0.8741 (p0) cc_final: 0.8504 (p0)
REVERT: G    7 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8533 (tttt)
REVERT: G   39 THR cc_start: 0.9029 (m) cc_final: 0.8757 (p)
REVERT: G   49 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8470 (mm-30)
REVERT: F    4 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (pp)
REVERT: F    9 MET cc_start: 0.8699 (tpp) cc_final: 0.8461 (tpp)
REVERT: E    6 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8460 (mmmt)
REVERT: E    9 MET cc_start: 0.8472 (ppp) cc_final: 0.8191 (ppp)
REVERT: D    4 LEU cc_start: 0.7150 (mm) cc_final: 0.6922 (mt)
REVERT: D    7 LYS cc_start: 0.9410 (mttt) cc_final: 0.8532 (tmtt)
REVERT: D    9 MET cc_start: 0.8079 (tpp) cc_final: 0.7782 (mmp)
REVERT: C    9 MET cc_start: 0.8133 (mmm) cc_final: 0.7922 (mpp)
REVERT: C   15 MET cc_start: 0.8513 (mmm) cc_final: 0.8011 (tpp)
REVERT: C   31 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (m-10)
  outliers start: 29
  outliers final: 16
  residues processed: 230
  average time/residue: 0.1462
  time to fit residues: 45.0241
Evaluate side-chains
  217 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 197
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.107690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.086813 restraints weight = 12472.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089886 restraints weight = 7914.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.090858 restraints weight = 5598.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5720  Z= 0.193
  Angle     :  0.707   9.609   7700  Z= 0.359
  Chirality :  0.043   0.217    899
  Planarity :  0.003   0.025    952
  Dihedral  :  5.565  56.167    765
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.56 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 22.62 %
    Favored  : 72.11 %
  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:  0.19 (0.32), residues: 723
  helix:  1.10 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -2.56 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 127 
 HIS   0.003   0.001   HIS E  30 
 PHE   0.015   0.001   PHE E  11 
 TYR   0.030   0.002   TYR A 219 
 ARG   0.001   0.000   ARG A   9 

*********************** 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
  254 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 223
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.7005 (OUTLIER) cc_final: 0.6680 (p)
REVERT: A   31 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7856 (pt0)
REVERT: A   74 LYS cc_start: 0.8888 (tptt) cc_final: 0.8585 (tmmt)
REVERT: A   77 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7651 (mm-30)
REVERT: A   81 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8861 (mptt)
REVERT: A   83 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: A   92 TYR cc_start: 0.8979 (t80) cc_final: 0.8585 (t80)
REVERT: A  145 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: A  217 ASP cc_start: 0.9048 (p0) cc_final: 0.8775 (p0)
REVERT: A  220 ASN cc_start: 0.8686 (m-40) cc_final: 0.8405 (m110)
REVERT: B   26 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7757 (mtm)
REVERT: G    7 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8507 (tttt)
REVERT: G   39 THR cc_start: 0.8926 (m) cc_final: 0.8523 (p)
REVERT: G   49 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8492 (mm-30)
REVERT: F    4 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8225 (pp)
REVERT: F    9 MET cc_start: 0.8745 (tpp) cc_final: 0.8479 (tpp)
REVERT: E    6 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8543 (mmmt)
REVERT: E    9 MET cc_start: 0.8497 (ppp) cc_final: 0.8267 (ppp)
REVERT: E   53 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8309 (m-80)
REVERT: D    7 LYS cc_start: 0.9404 (mttt) cc_final: 0.8535 (tmtt)
REVERT: D    9 MET cc_start: 0.8112 (tpp) cc_final: 0.7907 (mmp)
REVERT: C    9 MET cc_start: 0.8207 (mmm) cc_final: 0.8000 (mpp)
REVERT: C   15 MET cc_start: 0.8498 (mmm) cc_final: 0.8041 (tpp)
  outliers start: 31
  outliers final: 19
  residues processed: 236
  average time/residue: 0.1425
  time to fit residues: 45.1872
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  : 0.636 
-------------------------------------------------------------------------------
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 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   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 D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   25 LEU
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:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   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  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.109778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.088594 restraints weight = 12593.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.091671 restraints weight = 8266.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092974 restraints weight = 5870.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5720  Z= 0.195
  Angle     :  0.728  11.116   7700  Z= 0.367
  Chirality :  0.043   0.226    899
  Planarity :  0.003   0.025    952
  Dihedral  :  5.140  58.136    763
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 26.36 %
    Favored  : 68.71 %
  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:  0.32 (0.32), residues: 723
  helix:  1.15 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.59 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 127 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.025   0.001   PHE C  11 
 TYR   0.024   0.002   TYR B 147 
 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
  244 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 215
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6767 (OUTLIER) cc_final: 0.6498 (p)
REVERT: A   31 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7774 (pt0)
REVERT: A   74 LYS cc_start: 0.8864 (tptt) cc_final: 0.8584 (tmmt)
REVERT: A   77 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: A   81 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8765 (mptt)
REVERT: A   83 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8040 (tm-30)
REVERT: A   91 ASP cc_start: 0.7865 (m-30) cc_final: 0.7638 (m-30)
REVERT: A   92 TYR cc_start: 0.8918 (t80) cc_final: 0.8603 (t80)
REVERT: A  145 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8443 (mm-30)
REVERT: A  180 LYS cc_start: 0.8591 (mtmt) cc_final: 0.7702 (mtmt)
REVERT: A  217 ASP cc_start: 0.9036 (p0) cc_final: 0.8722 (p0)
REVERT: A  220 ASN cc_start: 0.8688 (m-40) cc_final: 0.8407 (m110)
REVERT: B   26 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7678 (mtm)
REVERT: B   99 GLN cc_start: 0.8715 (tt0) cc_final: 0.7908 (tm-30)
REVERT: B  116 GLU cc_start: 0.7477 (pt0) cc_final: 0.6403 (pt0)
REVERT: G    7 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8487 (tttt)
REVERT: F    4 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8279 (pp)
REVERT: F    9 MET cc_start: 0.8698 (tpp) cc_final: 0.8405 (tpp)
REVERT: F   30 HIS cc_start: 0.8055 (m170) cc_final: 0.7844 (m-70)
REVERT: E    6 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8512 (mmmt)
REVERT: E    9 MET cc_start: 0.8452 (ppp) cc_final: 0.8225 (ppp)
REVERT: E   53 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8229 (m-10)
REVERT: D    7 LYS cc_start: 0.9401 (mttt) cc_final: 0.8559 (tmtt)
REVERT: C   15 MET cc_start: 0.8474 (mmm) cc_final: 0.8072 (mmm)
  outliers start: 29
  outliers final: 18
  residues processed: 228
  average time/residue: 0.1386
  time to fit residues: 42.6021
Evaluate side-chains
  231 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
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 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 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    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:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.109055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.087496 restraints weight = 12674.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090387 restraints weight = 8471.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.090607 restraints weight = 6690.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3448

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= 0.216
  Angle     :  0.753  11.758   7700  Z= 0.380
  Chirality :  0.044   0.238    899
  Planarity :  0.003   0.023    952
  Dihedral  :  5.023  59.415    761
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 27.72 %
    Favored  : 67.52 %
  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:  0.49 (0.32), residues: 723
  helix:  1.24 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -2.36 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 207 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.022   0.001   PHE G  31 
 TYR   0.046   0.002   TYR A 219 
 ARG   0.005   0.001   ARG B 120 

*********************** 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
  234 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 206
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.6454 (p)
REVERT: A   31 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7957 (pt0)
REVERT: A   74 LYS cc_start: 0.8857 (tptt) cc_final: 0.8596 (tmmt)
REVERT: A   77 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: A   81 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8889 (mptt)
REVERT: A   83 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A   91 ASP cc_start: 0.7875 (m-30) cc_final: 0.7655 (m-30)
REVERT: A   92 TYR cc_start: 0.8937 (t80) cc_final: 0.8617 (t80)
REVERT: A  145 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8507 (mm-30)
REVERT: A  180 LYS cc_start: 0.8636 (mtmt) cc_final: 0.7866 (mtmt)
REVERT: A  217 ASP cc_start: 0.9022 (p0) cc_final: 0.8697 (p0)
REVERT: A  220 ASN cc_start: 0.8682 (m-40) cc_final: 0.8401 (m110)
REVERT: B   26 MET cc_start: 0.8126 (mtp) cc_final: 0.6867 (mtm)
REVERT: B   99 GLN cc_start: 0.8755 (tt0) cc_final: 0.7906 (tm-30)
REVERT: G    7 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8444 (tttt)
REVERT: F    4 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8306 (pp)
REVERT: F    9 MET cc_start: 0.8692 (tpp) cc_final: 0.8422 (tpp)
REVERT: E    6 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8520 (mmmt)
REVERT: E    9 MET cc_start: 0.8490 (ppp) cc_final: 0.8213 (ppp)
REVERT: E   53 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8224 (m-10)
REVERT: D    7 LYS cc_start: 0.9407 (mttt) cc_final: 0.8585 (tmtt)
REVERT: C   15 MET cc_start: 0.8457 (mmm) cc_final: 0.8042 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 217
  average time/residue: 0.1468
  time to fit residues: 42.5856
Evaluate side-chains
  221 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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 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   41 MET
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 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:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0470
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.110576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.089184 restraints weight = 12626.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.091919 restraints weight = 8736.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.092737 restraints weight = 6700.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5720  Z= 0.196
  Angle     :  0.764  11.902   7700  Z= 0.379
  Chirality :  0.044   0.230    899
  Planarity :  0.003   0.024    952
  Dihedral  :  4.959  59.113    761
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 28.06 %
    Favored  : 66.84 %
  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:  0.54 (0.32), residues: 723
  helix:  1.25 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.30 (0.47), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 127 
 HIS   0.002   0.001   HIS E  30 
 PHE   0.019   0.001   PHE G  31 
 TYR   0.015   0.001   TYR D  13 
 ARG   0.003   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
  237 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6243 (OUTLIER) cc_final: 0.5970 (p)
REVERT: A   31 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7848 (pt0)
REVERT: A   74 LYS cc_start: 0.8845 (tptt) cc_final: 0.8581 (tmmt)
REVERT: A   77 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7571 (mm-30)
REVERT: A   81 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8883 (mptt)
REVERT: A   83 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8009 (tm-30)
REVERT: A   91 ASP cc_start: 0.7840 (m-30) cc_final: 0.7610 (m-30)
REVERT: A   92 TYR cc_start: 0.8907 (t80) cc_final: 0.8568 (t80)
REVERT: A  145 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: A  180 LYS cc_start: 0.8554 (mtmt) cc_final: 0.7996 (mtmt)
REVERT: A  217 ASP cc_start: 0.9008 (p0) cc_final: 0.8680 (p0)
REVERT: A  220 ASN cc_start: 0.8637 (m-40) cc_final: 0.8358 (m110)
REVERT: B   26 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7515 (mtm)
REVERT: B   99 GLN cc_start: 0.8734 (tt0) cc_final: 0.8086 (tm-30)
REVERT: B  118 MET cc_start: 0.8576 (mtt) cc_final: 0.8328 (mtt)
REVERT: G    7 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8347 (ttpt)
REVERT: F    4 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (pp)
REVERT: F    9 MET cc_start: 0.8691 (tpp) cc_final: 0.8415 (tpp)
REVERT: E    6 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8521 (mmmt)
REVERT: E    9 MET cc_start: 0.8516 (ppp) cc_final: 0.8244 (ppp)
REVERT: E   53 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8165 (m-80)
REVERT: D    7 LYS cc_start: 0.9414 (mttt) cc_final: 0.8610 (tmtt)
REVERT: C   15 MET cc_start: 0.8366 (mmm) cc_final: 0.7970 (mmm)
  outliers start: 30
  outliers final: 19
  residues processed: 219
  average time/residue: 0.1446
  time to fit residues: 42.4107
Evaluate side-chains
  222 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  128 PHE
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   61 VAL
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   41 MET
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0570
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3597 r_free = 0.3597 target = 0.111590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.089837 restraints weight = 12525.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.092862 restraints weight = 8920.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093233 restraints weight = 6877.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3822

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= 0.196
  Angle     :  0.772  11.847   7700  Z= 0.381
  Chirality :  0.044   0.223    899
  Planarity :  0.003   0.023    952
  Dihedral  :  4.917  58.253    761
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.70 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 29.08 %
    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:  0.73 (0.32), residues: 723
  helix:  1.43 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.26 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 127 
 HIS   0.001   0.001   HIS C  30 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.017   0.001   TYR F  13 
 ARG   0.003   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
  240 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6042 (OUTLIER) cc_final: 0.5782 (p)
REVERT: A   31 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7867 (pt0)
REVERT: A   74 LYS cc_start: 0.8852 (tptt) cc_final: 0.8599 (tmmt)
REVERT: A   77 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: A   81 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8889 (mptt)
REVERT: A   83 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: A   91 ASP cc_start: 0.7774 (m-30) cc_final: 0.7538 (m-30)
REVERT: A   92 TYR cc_start: 0.8868 (t80) cc_final: 0.8573 (t80)
REVERT: A  145 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: A  180 LYS cc_start: 0.8544 (mtmt) cc_final: 0.7985 (mtmt)
REVERT: A  217 ASP cc_start: 0.9014 (p0) cc_final: 0.8626 (p0)
REVERT: A  220 ASN cc_start: 0.8621 (m-40) cc_final: 0.8286 (m110)
REVERT: B   26 MET cc_start: 0.7922 (mtp) cc_final: 0.7484 (mtm)
REVERT: B   99 GLN cc_start: 0.8692 (tt0) cc_final: 0.8126 (tm-30)
REVERT: B  118 MET cc_start: 0.8549 (mtt) cc_final: 0.8304 (mtt)
REVERT: B  210 ASP cc_start: 0.8297 (t0) cc_final: 0.7920 (t70)
REVERT: G    7 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8455 (mmtt)
REVERT: F    4 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8260 (pp)
REVERT: F    9 MET cc_start: 0.8681 (tpp) cc_final: 0.8411 (tpp)
REVERT: E    6 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8560 (mmmt)
REVERT: E    9 MET cc_start: 0.8494 (ppp) cc_final: 0.8264 (ppp)
REVERT: E   53 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8125 (m-80)
REVERT: D    7 LYS cc_start: 0.9404 (mttt) cc_final: 0.8586 (tmtt)
REVERT: C   15 MET cc_start: 0.8317 (mmm) cc_final: 0.7936 (mmm)
  outliers start: 27
  outliers final: 19
  residues processed: 223
  average time/residue: 0.1413
  time to fit residues: 42.2585
Evaluate side-chains
  231 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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 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   61 VAL
Chi-restraints excluded: chain F residue    4 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 D residue   55 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
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:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.108444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.086654 restraints weight = 12538.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.090997 restraints weight = 8902.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091129 restraints weight = 5466.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5720  Z= 0.273
  Angle     :  0.796  12.001   7700  Z= 0.400
  Chirality :  0.045   0.240    899
  Planarity :  0.004   0.068    952
  Dihedral  :  4.973  57.777    761
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 29.25 %
    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:  0.68 (0.32), residues: 723
  helix:  1.37 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -2.35 (0.47), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 127 
 HIS   0.002   0.001   HIS C  30 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.019   0.002   TYR B 147 
 ARG   0.003   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
  234 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 207
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6498 (OUTLIER) cc_final: 0.6200 (p)
REVERT: A   31 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7933 (pt0)
REVERT: A   74 LYS cc_start: 0.8886 (tptt) cc_final: 0.8635 (tmmt)
REVERT: A   77 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7602 (mm-30)
REVERT: A   81 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8890 (mptt)
REVERT: A   83 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7425 (tp40)
REVERT: A   91 ASP cc_start: 0.7933 (m-30) cc_final: 0.7692 (m-30)
REVERT: A   92 TYR cc_start: 0.9000 (t80) cc_final: 0.8682 (t80)
REVERT: A  145 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8553 (mm-30)
REVERT: A  151 ILE cc_start: 0.8186 (mm) cc_final: 0.7967 (mm)
REVERT: A  180 LYS cc_start: 0.8563 (mtmt) cc_final: 0.7969 (mtmt)
REVERT: A  217 ASP cc_start: 0.9035 (p0) cc_final: 0.8667 (p0)
REVERT: A  220 ASN cc_start: 0.8680 (m-40) cc_final: 0.8345 (m110)
REVERT: B   26 MET cc_start: 0.8018 (mtp) cc_final: 0.7610 (mtm)
REVERT: B   96 LEU cc_start: 0.9188 (mt) cc_final: 0.8690 (mp)
REVERT: B   99 GLN cc_start: 0.8678 (tt0) cc_final: 0.8195 (tm-30)
REVERT: G    7 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8455 (tttt)
REVERT: F    4 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8363 (pp)
REVERT: F    9 MET cc_start: 0.8728 (tpp) cc_final: 0.8477 (tpp)
REVERT: E    6 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8559 (mmmt)
REVERT: E    9 MET cc_start: 0.8468 (ppp) cc_final: 0.8248 (ppp)
REVERT: E   53 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8157 (m-80)
REVERT: D    7 LYS cc_start: 0.9449 (mttt) cc_final: 0.8639 (tmtt)
REVERT: C   15 MET cc_start: 0.8420 (mmm) cc_final: 0.8014 (mmm)
  outliers start: 27
  outliers final: 21
  residues processed: 219
  average time/residue: 0.1492
  time to fit residues: 44.6062
Evaluate side-chains
  228 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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 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   61 VAL
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 D residue   55 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   21 ILE
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:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3579 r_free = 0.3579 target = 0.110377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.088992 restraints weight = 12593.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091692 restraints weight = 8911.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.092221 restraints weight = 6902.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5720  Z= 0.220
  Angle     :  0.809  12.311   7700  Z= 0.403
  Chirality :  0.046   0.242    899
  Planarity :  0.004   0.061    952
  Dihedral  :  4.954  55.941    761
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.56 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 29.42 %
    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:  0.78 (0.32), residues: 723
  helix:  1.46 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.31 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 127 
 HIS   0.002   0.001   HIS D  30 
 PHE   0.018   0.001   PHE G  31 
 TYR   0.022   0.001   TYR B 147 
 ARG   0.003   0.001   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
  241 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 215
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6117 (OUTLIER) cc_final: 0.5816 (p)
REVERT: A   31 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8008 (pt0)
REVERT: A   74 LYS cc_start: 0.8861 (tptt) cc_final: 0.8611 (tmmt)
REVERT: A   77 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7564 (mm-30)
REVERT: A   91 ASP cc_start: 0.7888 (m-30) cc_final: 0.7666 (m-30)
REVERT: A   92 TYR cc_start: 0.8923 (t80) cc_final: 0.8577 (t80)
REVERT: A  105 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8151 (pm20)
REVERT: A  145 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8569 (mm-30)
REVERT: A  151 ILE cc_start: 0.8148 (mm) cc_final: 0.7926 (mm)
REVERT: A  180 LYS cc_start: 0.8553 (mtmt) cc_final: 0.7958 (mtmt)
REVERT: A  217 ASP cc_start: 0.9034 (p0) cc_final: 0.8738 (p0)
REVERT: A  220 ASN cc_start: 0.8646 (m-40) cc_final: 0.8323 (m110)
REVERT: B   26 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7532 (mtm)
REVERT: B   99 GLN cc_start: 0.8696 (tt0) cc_final: 0.8135 (tm-30)
REVERT: G    7 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8435 (tttt)
REVERT: F    4 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (pp)
REVERT: F    9 MET cc_start: 0.8730 (tpp) cc_final: 0.8462 (tpp)
REVERT: E    6 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8585 (mmmt)
REVERT: E    9 MET cc_start: 0.8535 (ppp) cc_final: 0.8270 (ppp)
REVERT: E   53 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8102 (m-80)
REVERT: D    7 LYS cc_start: 0.9453 (mttt) cc_final: 0.8679 (tmtt)
REVERT: C   15 MET cc_start: 0.8349 (mmm) cc_final: 0.7934 (mmm)
  outliers start: 26
  outliers final: 19
  residues processed: 226
  average time/residue: 0.1365
  time to fit residues: 41.8420
Evaluate side-chains
  233 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
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 B residue   26 MET
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   61 VAL
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 D residue   55 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
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:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:   20.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3577 r_free = 0.3577 target = 0.110018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.088483 restraints weight = 12661.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.091406 restraints weight = 8982.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.091868 restraints weight = 6782.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
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      :  0.004   0.036   5720  Z= 0.243
  Angle     :  0.830  11.945   7700  Z= 0.415
  Chirality :  0.047   0.241    899
  Planarity :  0.004   0.057    952
  Dihedral  :  4.932  52.222    761
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 29.76 %
    Favored  : 65.82 %
  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:  0.91 (0.32), residues: 723
  helix:  1.52 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.13 (0.48), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 127 
 HIS   0.001   0.001   HIS A  80 
 PHE   0.017   0.001   PHE G  31 
 TYR   0.013   0.001   TYR B 147 
 ARG   0.003   0.000   ARG B 120 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.34 seconds
wall clock time: 33 minutes 47.28 seconds (2027.28 seconds total)