Starting phenix.real_space_refine
on Tue Mar  3 13:44:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_10893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_10893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_10893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_10893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ys8_10893/03_2026/6ys8_10893.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.25, per 1000 atoms: 0.22
  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: 0.44
  Conformation dependent library (CDL) restraints added in 307.2 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: 0.17
  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: 0.86

  Time building geometry restraints manager: 0.61 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.650
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.250
-------------------------------------------------------------------------------
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= 0.319
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG B   9 
 TYR   0.017   0.002   TYR A  92 
 PHE   0.021   0.002   PHE A  20 
 TRP   0.006   0.002   TRP B 127 
 HIS   0.004   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 5720)
  covalent geometry    : angle       1.03486 ( 7700)
  hydrogen bonds       : bond        0.12942 (  423)
  hydrogen bonds       : angle       6.35642 ( 1260)

*********************** 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  : 0.227 
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: 0.8589 (tm-30) cc_final: 0.7915 (tp40)
REVERT: A  145 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8297 (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: 0.8701 (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: 0.8318 (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: 0.0713
  time to fit residues: 23.4607
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  : 0.224 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.105173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.083959 restraints weight = 12265.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086768 restraints weight = 7799.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.087911 restraints weight = 5620.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.089049 restraints weight = 4502.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.089303 restraints weight = 3796.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5720  Z= 0.169
  Angle     :  0.713   8.863   7700  Z= 0.379
  Chirality :  0.042   0.181    899
  Planarity :  0.004   0.032    952
  Dihedral  :  6.442  54.714    776
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.56 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.84 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.29), residues: 723
  helix: -0.04 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -3.12 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 120 
 TYR   0.018   0.002   TYR B 147 
 PHE   0.025   0.002   PHE D  31 
 TRP   0.010   0.001   TRP B 127 
 HIS   0.002   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5720)
  covalent geometry    : angle       0.71274 ( 7700)
  hydrogen bonds       : bond        0.04508 (  423)
  hydrogen bonds       : angle       4.50820 ( 1260)

*********************** 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
  243 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 225
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.7357 (ttp) cc_final: 0.5817 (tpp)
REVERT: A   31 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8179 (pt0)
REVERT: A   44 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8019 (mp0)
REVERT: A   74 LYS cc_start: 0.8911 (tptt) cc_final: 0.8581 (tmmt)
REVERT: A   83 GLN cc_start: 0.8573 (tm-30) cc_final: 0.7810 (tp40)
REVERT: A  145 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8263 (mm-30)
REVERT: A  146 LYS cc_start: 0.8606 (tttm) cc_final: 0.8286 (ttpt)
REVERT: A  217 ASP cc_start: 0.9019 (p0) cc_final: 0.8816 (p0)
REVERT: A  220 ASN cc_start: 0.8671 (m-40) cc_final: 0.8444 (m110)
REVERT: B   16 MET cc_start: 0.9411 (mmm) cc_final: 0.9172 (mmp)
REVERT: B   99 GLN cc_start: 0.8652 (tt0) cc_final: 0.7638 (tm-30)
REVERT: B  123 ASN cc_start: 0.8748 (p0) cc_final: 0.7493 (p0)
REVERT: B  124 ILE cc_start: 0.8384 (pt) cc_final: 0.8051 (pt)
REVERT: G    7 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8554 (tttt)
REVERT: G   49 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7907 (mm-30)
REVERT: F    4 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8082 (pp)
REVERT: F    9 MET cc_start: 0.8741 (tpp) cc_final: 0.8475 (tpp)
REVERT: D    4 LEU cc_start: 0.7138 (mm) cc_final: 0.6912 (mt)
REVERT: D    7 LYS cc_start: 0.9392 (mttt) cc_final: 0.8518 (tmtt)
REVERT: D    9 MET cc_start: 0.7980 (tpp) cc_final: 0.7672 (mmp)
REVERT: C    9 MET cc_start: 0.8105 (mmm) cc_final: 0.7844 (mpp)
REVERT: C   15 MET cc_start: 0.8449 (mmm) cc_final: 0.7987 (tpp)
REVERT: C   31 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7821 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 232
  average time/residue: 0.0608
  time to fit residues: 19.1641
Evaluate side-chains
  220 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  124 ILE
Chi-restraints excluded: chain A residue  138 ASN
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain G residue   25 LEU
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   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 43 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.106587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.085167 restraints weight = 12260.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.088090 restraints weight = 7896.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.089294 restraints weight = 5618.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.090241 restraints weight = 4531.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.090564 restraints weight = 3905.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2643

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= 0.151
  Angle     :  0.701   9.824   7700  Z= 0.366
  Chirality :  0.043   0.188    899
  Planarity :  0.004   0.026    952
  Dihedral  :  5.775  53.273    765
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.56 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.31), residues: 723
  helix:  0.77 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.74 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.020   0.002   TYR A 147 
 PHE   0.017   0.001   PHE E  11 
 TRP   0.008   0.001   TRP B 127 
 HIS   0.002   0.001   HIS E  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5720)
  covalent geometry    : angle       0.70068 ( 7700)
  hydrogen bonds       : bond        0.04332 (  423)
  hydrogen bonds       : angle       4.19688 ( 1260)

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

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.7278 (OUTLIER) cc_final: 0.7001 (p)
REVERT: A   31 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7976 (pt0)
REVERT: A   74 LYS cc_start: 0.8912 (tptt) cc_final: 0.8587 (tmmt)
REVERT: A   81 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8836 (mptt)
REVERT: A   92 TYR cc_start: 0.8994 (t80) cc_final: 0.8564 (t80)
REVERT: A  145 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: A  217 ASP cc_start: 0.9008 (p0) cc_final: 0.8755 (p0)
REVERT: A  220 ASN cc_start: 0.8679 (m-40) cc_final: 0.8412 (m110)
REVERT: B   16 MET cc_start: 0.9343 (mmm) cc_final: 0.9061 (mmp)
REVERT: B   26 MET cc_start: 0.8177 (mtp) cc_final: 0.7706 (mtm)
REVERT: B  123 ASN cc_start: 0.8717 (p0) cc_final: 0.8472 (p0)
REVERT: G    7 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8537 (tttt)
REVERT: G   39 THR cc_start: 0.9018 (m) cc_final: 0.8735 (p)
REVERT: G   49 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8441 (mm-30)
REVERT: F    4 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (pp)
REVERT: F    9 MET cc_start: 0.8679 (tpp) cc_final: 0.8447 (tpp)
REVERT: E    6 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8464 (mmmt)
REVERT: E    9 MET cc_start: 0.8456 (ppp) cc_final: 0.8184 (ppp)
REVERT: D    4 LEU cc_start: 0.7137 (mm) cc_final: 0.6919 (mt)
REVERT: D    7 LYS cc_start: 0.9408 (mttt) cc_final: 0.8530 (tmtt)
REVERT: D    9 MET cc_start: 0.8058 (tpp) cc_final: 0.7757 (mmp)
REVERT: C    9 MET cc_start: 0.8074 (mmm) cc_final: 0.7873 (mpp)
REVERT: C   15 MET cc_start: 0.8494 (mmm) cc_final: 0.7993 (tpp)
REVERT: C   31 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7648 (m-80)
  outliers start: 28
  outliers final: 17
  residues processed: 232
  average time/residue: 0.0646
  time to fit residues: 20.4578
Evaluate side-chains
  217 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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 B residue   17 TYR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain G residue   42 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   55 LEU
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 38 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0040
   overall best weight:    0.6992

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.107394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.086539 restraints weight = 12189.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.089318 restraints weight = 7865.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.090527 restraints weight = 5648.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.091586 restraints weight = 4503.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.091977 restraints weight = 3839.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5720  Z= 0.144
  Angle     :  0.700   9.582   7700  Z= 0.357
  Chirality :  0.042   0.218    899
  Planarity :  0.003   0.026    952
  Dihedral  :  5.578  55.849    765
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.56 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.64 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.32), residues: 723
  helix:  1.08 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -2.60 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.027   0.002   TYR A 219 
 PHE   0.016   0.001   PHE B  89 
 TRP   0.002   0.000   TRP A 207 
 HIS   0.003   0.001   HIS E  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5720)
  covalent geometry    : angle       0.69994 ( 7700)
  hydrogen bonds       : bond        0.04229 (  423)
  hydrogen bonds       : angle       4.13182 ( 1260)

*********************** 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: 29
    poor density    : 225
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6664 (p)
REVERT: A   31 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7830 (pt0)
REVERT: A   74 LYS cc_start: 0.8884 (tptt) cc_final: 0.8585 (tmmt)
REVERT: A   77 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: A   81 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8862 (mptt)
REVERT: A   92 TYR cc_start: 0.8964 (t80) cc_final: 0.8566 (t80)
REVERT: A  145 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8401 (mm-30)
REVERT: A  146 LYS cc_start: 0.8517 (tttm) cc_final: 0.8259 (mtmt)
REVERT: A  217 ASP cc_start: 0.9016 (p0) cc_final: 0.8726 (p0)
REVERT: A  220 ASN cc_start: 0.8718 (m-40) cc_final: 0.8469 (m110)
REVERT: B   26 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7657 (mtm)
REVERT: B   92 TYR cc_start: 0.8700 (t80) cc_final: 0.8144 (t80)
REVERT: G    7 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8500 (tttt)
REVERT: G   39 THR cc_start: 0.8924 (m) cc_final: 0.8526 (p)
REVERT: G   49 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8473 (mm-30)
REVERT: F    4 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8241 (pp)
REVERT: F    9 MET cc_start: 0.8699 (tpp) cc_final: 0.8436 (tpp)
REVERT: E    6 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8433 (mmmt)
REVERT: E    9 MET cc_start: 0.8443 (ppp) cc_final: 0.8207 (ppp)
REVERT: E   53 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8272 (m-80)
REVERT: D    7 LYS cc_start: 0.9408 (mttt) cc_final: 0.8527 (tmtt)
REVERT: C   15 MET cc_start: 0.8486 (mmm) cc_final: 0.8024 (tpp)
  outliers start: 29
  outliers final: 18
  residues processed: 239
  average time/residue: 0.0612
  time to fit residues: 19.9995
Evaluate side-chains
  226 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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    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   36 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.109735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.088551 restraints weight = 12708.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.090545 restraints weight = 8301.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.091123 restraints weight = 6268.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093567 restraints weight = 5315.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093552 restraints weight = 3983.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5720  Z= 0.143
  Angle     :  0.719   9.467   7700  Z= 0.367
  Chirality :  0.043   0.220    899
  Planarity :  0.003   0.024    952
  Dihedral  :  5.172  57.565    763
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.87 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.32), residues: 723
  helix:  1.20 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.59 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   9 
 TYR   0.026   0.002   TYR B 147 
 PHE   0.026   0.001   PHE C  11 
 TRP   0.002   0.001   TRP B 207 
 HIS   0.002   0.001   HIS E  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5720)
  covalent geometry    : angle       0.71870 ( 7700)
  hydrogen bonds       : bond        0.04220 (  423)
  hydrogen bonds       : angle       4.10768 ( 1260)

*********************** 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
  247 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 217
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6855 (OUTLIER) cc_final: 0.6558 (p)
REVERT: A   31 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7729 (pt0)
REVERT: A   74 LYS cc_start: 0.8862 (tptt) cc_final: 0.8574 (tmmt)
REVERT: A   77 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: A   81 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8764 (mptt)
REVERT: A   91 ASP cc_start: 0.7872 (m-30) cc_final: 0.7649 (m-30)
REVERT: A   92 TYR cc_start: 0.8939 (t80) cc_final: 0.8608 (t80)
REVERT: A  145 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8391 (mm-30)
REVERT: A  146 LYS cc_start: 0.8484 (tttm) cc_final: 0.8251 (mtmt)
REVERT: A  180 LYS cc_start: 0.8586 (mtmt) cc_final: 0.7693 (mtmt)
REVERT: A  217 ASP cc_start: 0.8954 (p0) cc_final: 0.8633 (p0)
REVERT: A  220 ASN cc_start: 0.8671 (m-40) cc_final: 0.8409 (m110)
REVERT: B   26 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7651 (mtm)
REVERT: B   99 GLN cc_start: 0.8717 (tt0) cc_final: 0.7915 (tm-30)
REVERT: B  116 GLU cc_start: 0.7535 (pt0) cc_final: 0.6459 (pt0)
REVERT: G    7 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8505 (tttt)
REVERT: F    4 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8292 (pp)
REVERT: F    9 MET cc_start: 0.8666 (tpp) cc_final: 0.8398 (tpp)
REVERT: E    6 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8518 (mmmt)
REVERT: E    9 MET cc_start: 0.8461 (ppp) cc_final: 0.8214 (ppp)
REVERT: E   53 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8195 (m-80)
REVERT: D    7 LYS cc_start: 0.9405 (mttt) cc_final: 0.8578 (tmtt)
REVERT: C   15 MET cc_start: 0.8422 (mmm) cc_final: 0.8037 (mmm)
REVERT: C   59 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5466 (tt0)
  outliers start: 30
  outliers final: 19
  residues processed: 230
  average time/residue: 0.0587
  time to fit residues: 18.5188
Evaluate side-chains
  229 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  140 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain G residue   22 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0020
   chunk 57 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.3996

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.107153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.086590 restraints weight = 12576.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.089405 restraints weight = 8451.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089704 restraints weight = 6493.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.090890 restraints weight = 5186.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.091393 restraints weight = 4307.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3387

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= 0.177
  Angle     :  0.760  11.485   7700  Z= 0.384
  Chirality :  0.044   0.228    899
  Planarity :  0.003   0.023    952
  Dihedral  :  5.065  59.547    761
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  4.98 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 26.36 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.32), residues: 723
  helix:  1.29 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -2.47 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   9 
 TYR   0.045   0.002   TYR A 219 
 PHE   0.020   0.001   PHE G  31 
 TRP   0.007   0.001   TRP B 207 
 HIS   0.002   0.001   HIS E  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5720)
  covalent geometry    : angle       0.76014 ( 7700)
  hydrogen bonds       : bond        0.04332 (  423)
  hydrogen bonds       : angle       4.23728 ( 1260)

*********************** 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
  241 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 208
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7964 (pt0)
REVERT: A   74 LYS cc_start: 0.8869 (tptt) cc_final: 0.8607 (tmmt)
REVERT: A   77 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7568 (mm-30)
REVERT: A   81 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8867 (mptt)
REVERT: A   91 ASP cc_start: 0.7936 (m-30) cc_final: 0.7700 (m-30)
REVERT: A   92 TYR cc_start: 0.9003 (t80) cc_final: 0.8653 (t80)
REVERT: A  145 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8437 (mm-30)
REVERT: A  180 LYS cc_start: 0.8606 (mtmt) cc_final: 0.7766 (mtmt)
REVERT: A  217 ASP cc_start: 0.8981 (p0) cc_final: 0.8666 (p0)
REVERT: A  220 ASN cc_start: 0.8718 (m-40) cc_final: 0.8447 (m110)
REVERT: B   26 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7622 (mtm)
REVERT: B   99 GLN cc_start: 0.8731 (tt0) cc_final: 0.7903 (tm-30)
REVERT: G    7 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8431 (tttt)
REVERT: G   49 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8358 (mm-30)
REVERT: F    4 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8302 (pp)
REVERT: F    9 MET cc_start: 0.8696 (tpp) cc_final: 0.8437 (tpp)
REVERT: E    6 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8522 (mmmt)
REVERT: E    9 MET cc_start: 0.8435 (ppp) cc_final: 0.8176 (ppp)
REVERT: E   41 MET cc_start: 0.8714 (mtp) cc_final: 0.8450 (mtm)
REVERT: E   53 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8240 (m-10)
REVERT: D    7 LYS cc_start: 0.9421 (mttt) cc_final: 0.8604 (tmtt)
REVERT: C   15 MET cc_start: 0.8474 (mmm) cc_final: 0.8058 (mmm)
  outliers start: 33
  outliers final: 24
  residues processed: 222
  average time/residue: 0.0635
  time to fit residues: 19.2049
Evaluate side-chains
  223 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  151 ILE
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain G residue   61 VAL
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   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
Chi-restraints excluded: chain C residue   44 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 32 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.110446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.089240 restraints weight = 12613.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.091350 restraints weight = 8413.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.091934 restraints weight = 6363.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094393 restraints weight = 5371.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094404 restraints weight = 3981.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5720  Z= 0.142
  Angle     :  0.770  12.912   7700  Z= 0.380
  Chirality :  0.045   0.380    899
  Planarity :  0.003   0.023    952
  Dihedral  :  4.993  58.786    761
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.26 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.06 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.32), residues: 723
  helix:  1.23 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -2.41 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.053   0.002   TYR A 219 
 PHE   0.019   0.001   PHE G  31 
 TRP   0.014   0.001   TRP B 127 
 HIS   0.003   0.001   HIS F  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5720)
  covalent geometry    : angle       0.76985 ( 7700)
  hydrogen bonds       : bond        0.04189 (  423)
  hydrogen bonds       : angle       4.18108 ( 1260)

*********************** 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
  247 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 219
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6546 (OUTLIER) cc_final: 0.6244 (p)
REVERT: A   31 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7840 (pt0)
REVERT: A   74 LYS cc_start: 0.8834 (tptt) cc_final: 0.8575 (tmmt)
REVERT: A   77 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7532 (mm-30)
REVERT: A   81 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8865 (mptt)
REVERT: A   91 ASP cc_start: 0.7828 (m-30) cc_final: 0.7598 (m-30)
REVERT: A   92 TYR cc_start: 0.8928 (t80) cc_final: 0.8602 (t80)
REVERT: A  145 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8456 (mm-30)
REVERT: A  180 LYS cc_start: 0.8546 (mtmt) cc_final: 0.7964 (mtmt)
REVERT: A  217 ASP cc_start: 0.8951 (p0) cc_final: 0.8684 (p0)
REVERT: A  220 ASN cc_start: 0.8659 (m-40) cc_final: 0.8348 (m110)
REVERT: B   26 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7596 (mtm)
REVERT: B   99 GLN cc_start: 0.8697 (tt0) cc_final: 0.7875 (tm-30)
REVERT: B  220 ASN cc_start: 0.8661 (p0) cc_final: 0.8437 (t0)
REVERT: G    7 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8417 (tttt)
REVERT: G   49 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8278 (mm-30)
REVERT: F    4 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8341 (pp)
REVERT: F    9 MET cc_start: 0.8614 (tpp) cc_final: 0.8351 (tpp)
REVERT: E    6 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8521 (mmmt)
REVERT: E    9 MET cc_start: 0.8430 (ppp) cc_final: 0.8174 (ppp)
REVERT: E   53 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8172 (m-10)
REVERT: D    7 LYS cc_start: 0.9406 (mttt) cc_final: 0.8601 (tmtt)
REVERT: C   15 MET cc_start: 0.8305 (mmm) cc_final: 0.7899 (mmm)
  outliers start: 28
  outliers final: 16
  residues processed: 231
  average time/residue: 0.0612
  time to fit residues: 19.4574
Evaluate side-chains
  220 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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 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   48 THR
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.5558

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.089859 restraints weight = 12522.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.092760 restraints weight = 8878.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.093129 restraints weight = 6904.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.094408 restraints weight = 5609.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.095127 restraints weight = 4609.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3865

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= 0.145
  Angle     :  0.802  14.073   7700  Z= 0.392
  Chirality :  0.047   0.360    899
  Planarity :  0.004   0.065    952
  Dihedral  :  4.897  56.862    761
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 30.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.32), residues: 723
  helix:  1.32 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.29 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.051   0.002   TYR A 219 
 PHE   0.019   0.001   PHE G  31 
 TRP   0.013   0.001   TRP B 127 
 HIS   0.003   0.001   HIS F  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5720)
  covalent geometry    : angle       0.80188 ( 7700)
  hydrogen bonds       : bond        0.04184 (  423)
  hydrogen bonds       : angle       4.21278 ( 1260)

*********************** 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
  238 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6038 (OUTLIER) cc_final: 0.5768 (p)
REVERT: A   31 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7831 (pt0)
REVERT: A   74 LYS cc_start: 0.8845 (tptt) cc_final: 0.8596 (tmmt)
REVERT: A   77 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7539 (mm-30)
REVERT: A   91 ASP cc_start: 0.7856 (m-30) cc_final: 0.7620 (m-30)
REVERT: A   92 TYR cc_start: 0.8808 (t80) cc_final: 0.8545 (t80)
REVERT: A  145 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8493 (mm-30)
REVERT: A  180 LYS cc_start: 0.8567 (mtmt) cc_final: 0.7981 (mtmt)
REVERT: A  217 ASP cc_start: 0.9038 (p0) cc_final: 0.8648 (p0)
REVERT: A  220 ASN cc_start: 0.8686 (m110) cc_final: 0.8391 (m110)
REVERT: B   26 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7593 (mtm)
REVERT: B   96 LEU cc_start: 0.9127 (mt) cc_final: 0.8690 (mp)
REVERT: B   99 GLN cc_start: 0.8707 (tt0) cc_final: 0.7888 (tm-30)
REVERT: G    7 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8352 (ttpt)
REVERT: G   49 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8290 (mm-30)
REVERT: F    4 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8312 (pp)
REVERT: F    9 MET cc_start: 0.8700 (tpp) cc_final: 0.8421 (tpp)
REVERT: E    6 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8559 (mmmt)
REVERT: E    9 MET cc_start: 0.8423 (ppp) cc_final: 0.8205 (ppp)
REVERT: E   53 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8130 (m-80)
REVERT: D    7 LYS cc_start: 0.9416 (mttt) cc_final: 0.8613 (tmtt)
REVERT: C   15 MET cc_start: 0.8290 (mmm) cc_final: 0.7789 (mmm)
REVERT: C   27 LYS cc_start: 0.9146 (tttm) cc_final: 0.8804 (tttt)
  outliers start: 24
  outliers final: 15
  residues processed: 224
  average time/residue: 0.0606
  time to fit residues: 18.6965
Evaluate side-chains
  224 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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 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 F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   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   55 LEU
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   31 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.110989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.089008 restraints weight = 12589.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091919 restraints weight = 9118.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092704 restraints weight = 6823.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.093768 restraints weight = 5514.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.094331 restraints weight = 4682.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5720  Z= 0.158
  Angle     :  0.843  14.596   7700  Z= 0.411
  Chirality :  0.047   0.360    899
  Planarity :  0.004   0.057    952
  Dihedral  :  4.851  53.732    761
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.39 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 31.46 %
    Favored  : 64.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.32), residues: 723
  helix:  1.35 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -2.27 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.049   0.002   TYR A 219 
 PHE   0.019   0.001   PHE G  31 
 TRP   0.016   0.001   TRP B 127 
 HIS   0.003   0.001   HIS F  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5720)
  covalent geometry    : angle       0.84298 ( 7700)
  hydrogen bonds       : bond        0.04175 (  423)
  hydrogen bonds       : angle       4.28257 ( 1260)

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

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 SER cc_start: 0.6041 (OUTLIER) cc_final: 0.5791 (p)
REVERT: A   31 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7889 (pt0)
REVERT: A   39 MET cc_start: 0.8188 (mtm) cc_final: 0.7951 (mtm)
REVERT: A   74 LYS cc_start: 0.8850 (tptt) cc_final: 0.8591 (tmmt)
REVERT: A   91 ASP cc_start: 0.7851 (m-30) cc_final: 0.7627 (m-30)
REVERT: A   92 TYR cc_start: 0.8837 (t80) cc_final: 0.8599 (t80)
REVERT: A  105 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8140 (pm20)
REVERT: A  145 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8534 (mm-30)
REVERT: A  180 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8001 (mtmt)
REVERT: A  217 ASP cc_start: 0.9042 (p0) cc_final: 0.8645 (p0)
REVERT: A  219 TYR cc_start: 0.8823 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  220 ASN cc_start: 0.8651 (m110) cc_final: 0.8367 (m110)
REVERT: B   26 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7628 (mtm)
REVERT: B   99 GLN cc_start: 0.8682 (tt0) cc_final: 0.8090 (tm-30)
REVERT: G    7 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8439 (tttt)
REVERT: G   49 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8297 (mm-30)
REVERT: F    4 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8358 (pp)
REVERT: F    9 MET cc_start: 0.8678 (tpp) cc_final: 0.8396 (tpp)
REVERT: E    6 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8555 (mmmt)
REVERT: E    9 MET cc_start: 0.8431 (ppp) cc_final: 0.8229 (ppp)
REVERT: E   53 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8110 (m-80)
REVERT: D    7 LYS cc_start: 0.9442 (mttt) cc_final: 0.8665 (tmtt)
REVERT: C   15 MET cc_start: 0.8256 (mmm) cc_final: 0.7779 (mmm)
REVERT: C   27 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8788 (tttt)
REVERT: C   59 GLU cc_start: 0.7125 (mp0) cc_final: 0.6906 (tp30)
  outliers start: 23
  outliers final: 16
  residues processed: 219
  average time/residue: 0.0596
  time to fit residues: 18.0970
Evaluate side-chains
  232 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 210
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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 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   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 VAL
Chi-restraints excluded: chain C residue   27 LYS
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 57 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090388 restraints weight = 12690.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093317 restraints weight = 9048.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.094007 restraints weight = 6816.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.095015 restraints weight = 5482.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.095678 restraints weight = 4706.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4158

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= 0.151
  Angle     :  0.855  14.589   7700  Z= 0.412
  Chirality :  0.046   0.324    899
  Planarity :  0.004   0.054    952
  Dihedral  :  4.783  52.542    761
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 31.46 %
    Favored  : 64.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.32), residues: 723
  helix:  1.38 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -2.20 (0.48), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.047   0.002   TYR A 219 
 PHE   0.019   0.001   PHE B 128 
 TRP   0.016   0.001   TRP B 127 
 HIS   0.002   0.001   HIS F  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5720)
  covalent geometry    : angle       0.85485 ( 7700)
  hydrogen bonds       : bond        0.04222 (  423)
  hydrogen bonds       : angle       4.27866 ( 1260)

********************** 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
  231 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7926 (pt0)
REVERT: A   74 LYS cc_start: 0.8866 (tptt) cc_final: 0.8611 (tmmt)
REVERT: A   91 ASP cc_start: 0.7830 (m-30) cc_final: 0.7606 (m-30)
REVERT: A   92 TYR cc_start: 0.8804 (t80) cc_final: 0.8576 (t80)
REVERT: A  105 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8150 (pm20)
REVERT: A  145 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8560 (mm-30)
REVERT: A  180 LYS cc_start: 0.8537 (mtmt) cc_final: 0.7979 (mtmt)
REVERT: A  217 ASP cc_start: 0.9058 (p0) cc_final: 0.8659 (p0)
REVERT: A  219 TYR cc_start: 0.8832 (m-80) cc_final: 0.8542 (m-80)
REVERT: A  220 ASN cc_start: 0.8675 (m110) cc_final: 0.8375 (m110)
REVERT: B   26 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7641 (mtm)
REVERT: B   99 GLN cc_start: 0.8721 (tt0) cc_final: 0.8142 (tm-30)
REVERT: G    7 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8422 (tttt)
REVERT: G   49 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8252 (mm-30)
REVERT: F    4 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8357 (pp)
REVERT: F    9 MET cc_start: 0.8667 (tpp) cc_final: 0.8393 (tpp)
REVERT: E    9 MET cc_start: 0.8428 (ppp) cc_final: 0.8212 (ppp)
REVERT: E   53 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8071 (m-80)
REVERT: D    7 LYS cc_start: 0.9448 (mttt) cc_final: 0.8687 (tmtt)
REVERT: C   15 MET cc_start: 0.8272 (mmm) cc_final: 0.7786 (mmm)
REVERT: C   27 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8768 (tttt)
  outliers start: 25
  outliers final: 16
  residues processed: 216
  average time/residue: 0.0603
  time to fit residues: 18.2104
Evaluate side-chains
  224 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  113 MET
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 B residue  177 VAL
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain F residue    4 LEU
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain E residue   53 PHE
Chi-restraints excluded: chain E residue   61 VAL
Chi-restraints excluded: chain D residue   61 VAL
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   27 LYS
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 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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  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 = 0.3615 r_free = 0.3615 target = 0.112659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.090471 restraints weight = 12394.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093515 restraints weight = 9082.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.094455 restraints weight = 6647.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095261 restraints weight = 5315.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.096044 restraints weight = 4840.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5720  Z= 0.157
  Angle     :  0.858  15.640   7700  Z= 0.418
  Chirality :  0.047   0.296    899
  Planarity :  0.004   0.052    952
  Dihedral  :  4.759  51.296    761
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  1.11 %
    Allowed  :  5.12 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 30.61 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.32), residues: 723
  helix:  1.35 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -2.18 (0.49), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.047   0.002   TYR A 219 
 PHE   0.017   0.001   PHE G  31 
 TRP   0.015   0.001   TRP B 127 
 HIS   0.002   0.001   HIS F  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5720)
  covalent geometry    : angle       0.85822 ( 7700)
  hydrogen bonds       : bond        0.04212 (  423)
  hydrogen bonds       : angle       4.28178 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1021.32 seconds
wall clock time: 18 minutes 25.11 seconds (1105.11 seconds total)