Starting phenix.real_space_refine
on Wed Mar 12 07:08:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9imh_60689/03_2025/9imh_60689.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
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=   0.003 sd=   0.855
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      36      5.16       5
     C    4842      2.51       5
     N    1272      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7674
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "B"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
    Chain: "C"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "D"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
    Chain: "E"
      Number of atoms: 1290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1290
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 9, 'TRANS': 151}
    Chain: "F"
      Number of atoms: 1268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1268
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 9, 'TRANS': 149}
  Time building chain proxies: 5.03, per 1000 atoms: 0.66
  Number of scatterers: 7674
  At special positions: 0
  Unit cell: (111.8, 107.9, 61.1, 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      36     16.00
     O    1524      8.00
     N    1272      7.00
     C    4842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 972.0 milliseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 14 sheets defined
      23.1% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 19
    Processing helix  chain 'A' and resid 85 through 103
    Processing helix  chain 'B' and resid 3 through 20
    Processing helix  chain 'B' and resid 85 through 103
    Processing helix  chain 'C' and resid 3 through 20
      removed outlier: 3.564A  pdb=" N   ASP C  20 " --> pdb=" O   SER C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 103
    Processing helix  chain 'D' and resid 3 through 20
    Processing helix  chain 'D' and resid 85 through 103
    Processing helix  chain 'E' and resid 3 through 20
    Processing helix  chain 'E' and resid 85 through 104
      removed outlier: 3.623A  pdb=" N   GLN E  89 " --> pdb=" O   ASP E  85 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY E 104 " --> pdb=" O   VAL E 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 20
      removed outlier: 3.503A  pdb=" N   ILE F   7 " --> pdb=" O   HIS F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 103
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53
      removed outlier: 3.983A  pdb=" N   MET A  70 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR A 152 " --> pdb=" O   MET A  70 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 148 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLU A 145 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   VAL A 131 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ASN A 147 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.546A  pdb=" N   TRP B  69 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.543A  pdb=" N   MET B  70 " --> pdb=" O   TYR B 152 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR B 152 " --> pdb=" O   MET B  70 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL B 148 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLU B 145 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   VAL B 131 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ASN B 147 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ARG B 151 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP B 125 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109
    Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 53
    Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53
      removed outlier: 3.658A  pdb=" N   MET C  70 " --> pdb=" O   TYR C 152 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR C 152 " --> pdb=" O   MET C  70 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LEU C 143 " --> pdb=" O   THR C 133 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   THR C 133 " --> pdb=" O   LEU C 143 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLU C 145 " --> pdb=" O   VAL C 131 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   VAL C 131 " --> pdb=" O   GLU C 145 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN C 147 " --> pdb=" O   THR C 129 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 53
    Processing sheet with id=AA9, first strand: chain 'D' and resid 51 through 53
      removed outlier: 3.594A  pdb=" N   MET D  70 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR D 152 " --> pdb=" O   MET D  70 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL D 148 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLU D 145 " --> pdb=" O   VAL D 131 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   VAL D 131 " --> pdb=" O   GLU D 145 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ASN D 147 " --> pdb=" O   THR D 129 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 51 through 53
    Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 53
      removed outlier: 3.633A  pdb=" N   MET E  70 " --> pdb=" O   TYR E 152 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL E 148 " --> pdb=" O   LEU E  74 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ASN E 147 " --> pdb=" O   THR E 129 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108
      removed outlier: 4.531A  pdb=" N   LEU E 107 " --> pdb=" O   ALA E 123 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 53
      removed outlier: 3.510A  pdb=" N   TRP F  69 " --> pdb=" O   GLN F  61 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 53
      removed outlier: 3.698A  pdb=" N   TYR F 152 " --> pdb=" O   MET F  70 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL F 148 " --> pdb=" O   LEU F  74 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL F  78 " --> pdb=" O   ALA F 144 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA F 144 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLU F 145 " --> pdb=" O   VAL F 131 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   VAL F 131 " --> pdb=" O   GLU F 145 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ASN F 147 " --> pdb=" O   THR F 129 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1335
        1.31 -     1.44: 2014
        1.44 -     1.56: 4415
        1.56 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 7830
  Sorted by residual:
  bond pdb=" CA  TYR A  50 "
       pdb=" C   TYR A  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.441  0.083 1.27e-02 6.20e+03 4.22e+01
  bond pdb=" CA  PHE A  48 "
       pdb=" CB  PHE A  48 "
    ideal  model  delta    sigma   weight residual
    1.530  1.439  0.091 1.58e-02 4.01e+03 3.33e+01
  bond pdb=" CA  PHE B  48 "
       pdb=" CB  PHE B  48 "
    ideal  model  delta    sigma   weight residual
    1.530  1.443  0.087 1.58e-02 4.01e+03 3.05e+01
  bond pdb=" CA  GLU D  47 "
       pdb=" C   GLU D  47 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.31e-02 5.83e+03 2.06e+01
  bond pdb=" CA  PRO E  49 "
       pdb=" CB  PRO E  49 "
    ideal  model  delta    sigma   weight residual
    1.533  1.469  0.064 1.42e-02 4.96e+03 2.04e+01
  ... (remaining 7825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 10364
        3.04 -     6.09: 214
        6.09 -     9.13: 43
        9.13 -    12.18: 4
       12.18 -    15.22: 1
  Bond angle restraints: 10626
  Sorted by residual:
  angle pdb=" N   PHE D  28 "
        pdb=" CA  PHE D  28 "
        pdb=" C   PHE D  28 "
      ideal   model   delta    sigma   weight residual
     107.62  122.84  -15.22 1.97e+00 2.58e-01 5.97e+01
  angle pdb=" C   GLU D  82 "
        pdb=" CA  GLU D  82 "
        pdb=" CB  GLU D  82 "
      ideal   model   delta    sigma   weight residual
     117.23  107.87    9.36 1.36e+00 5.41e-01 4.74e+01
  angle pdb=" CA  GLU D  82 "
        pdb=" C   GLU D  82 "
        pdb=" N   LYS D  83 "
      ideal   model   delta    sigma   weight residual
     119.98  114.84    5.14 8.50e-01 1.38e+00 3.66e+01
  angle pdb=" C   PRO C  49 "
        pdb=" N   TYR C  50 "
        pdb=" CA  TYR C  50 "
      ideal   model   delta    sigma   weight residual
     122.19  130.29   -8.10 1.41e+00 5.03e-01 3.30e+01
  angle pdb=" CA  PRO F  49 "
        pdb=" N   PRO F  49 "
        pdb=" CD  PRO F  49 "
      ideal   model   delta    sigma   weight residual
     112.00  104.68    7.32 1.40e+00 5.10e-01 2.73e+01
  ... (remaining 10621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4217
       17.88 -    35.76: 424
       35.76 -    53.64: 100
       53.64 -    71.52: 14
       71.52 -    89.41: 9
  Dihedral angle restraints: 4764
    sinusoidal: 1956
      harmonic: 2808
  Sorted by residual:
  dihedral pdb=" C   PHE D  48 "
           pdb=" N   PHE D  48 "
           pdb=" CA  PHE D  48 "
           pdb=" CB  PHE D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -148.93   26.33     0      2.50e+00 1.60e-01 1.11e+02
  dihedral pdb=" N   PHE D  48 "
           pdb=" C   PHE D  48 "
           pdb=" CA  PHE D  48 "
           pdb=" CB  PHE D  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  147.16  -24.36     0      2.50e+00 1.60e-01 9.50e+01
  dihedral pdb=" C   PHE F  48 "
           pdb=" N   PHE F  48 "
           pdb=" CA  PHE F  48 "
           pdb=" CB  PHE F  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.98   19.38     0      2.50e+00 1.60e-01 6.01e+01
  ... (remaining 4761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.232: 1171
       0.232 -    0.465: 4
       0.465 -    0.697: 4
       0.697 -    0.929: 2
       0.929 -    1.161: 1
  Chirality restraints: 1182
  Sorted by residual:
  chirality pdb=" CA  PHE D  48 "
            pdb=" N   PHE D  48 "
            pdb=" C   PHE D  48 "
            pdb=" CB  PHE D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.35    1.16 2.00e-01 2.50e+01 3.37e+01
  chirality pdb=" CA  PHE F  48 "
            pdb=" N   PHE F  48 "
            pdb=" C   PHE F  48 "
            pdb=" CB  PHE F  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.70    0.81 2.00e-01 2.50e+01 1.64e+01
  chirality pdb=" CA  PHE B  48 "
            pdb=" N   PHE B  48 "
            pdb=" C   PHE B  48 "
            pdb=" CB  PHE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.34e+01
  ... (remaining 1179 not shown)

  Planarity restraints: 1392
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F  48 "    0.106 5.00e-02 4.00e+02   1.57e-01 3.95e+01
        pdb=" N   PRO F  49 "   -0.272 5.00e-02 4.00e+02
        pdb=" CA  PRO F  49 "    0.085 5.00e-02 4.00e+02
        pdb=" CD  PRO F  49 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  48 "   -0.101 5.00e-02 4.00e+02   1.54e-01 3.78e+01
        pdb=" N   PRO D  49 "    0.266 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "   -0.084 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "   -0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  48 "   -0.096 5.00e-02 4.00e+02   1.47e-01 3.44e+01
        pdb=" N   PRO C  49 "    0.254 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.075 5.00e-02 4.00e+02
  ... (remaining 1389 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 445
        2.72 -     3.26: 7800
        3.26 -     3.81: 11681
        3.81 -     4.35: 13461
        4.35 -     4.90: 22994
  Nonbonded interactions: 56381
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  84 "
            pdb=" N   ASP D  85 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" O   THR B  39 "
            pdb=" OH  TYR B  50 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   THR D  39 "
            pdb=" OH  TYR D  50 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   LYS E  83 "
            pdb=" OG1 THR E  84 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   THR A  99 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.256 3.040
  ... (remaining 56376 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 159)
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 159)
  selection = chain 'D'
  selection = (chain 'E' and resid 1 through 159)
  selection = chain 'F'
}

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:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.850
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
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   0.091   7830  Z= 0.346
  Angle     :  1.059  15.223  10626  Z= 0.596
  Chirality :  0.078   1.161   1182
  Planarity :  0.011   0.157   1392
  Dihedral  : 15.415  89.406   2964
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  3.48 %
    Allowed  : 12.03 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.93 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.78 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.28), residues: 948
  helix:  0.75 (0.38), residues: 198
  sheet: -0.50 (0.29), residues: 333
  loop : -3.35 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.004   0.001   HIS D   3 
 PHE   0.029   0.002   PHE D  28 
 TYR   0.038   0.002   TYR B 109 
 ARG   0.005   0.000   ARG D 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 319
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7087 (m-40) cc_final: 0.6794 (m-40)
REVERT: A   80 ASP cc_start: 0.7572 (t0) cc_final: 0.6350 (t0)
REVERT: B   70 MET cc_start: 0.7965 (tpp) cc_final: 0.7541 (mtt)
REVERT: B   88 GLU cc_start: 0.7151 (tp30) cc_final: 0.6905 (tm-30)
REVERT: B  113 LYS cc_start: 0.6787 (tppt) cc_final: 0.6368 (tmmt)
REVERT: C   45 ILE cc_start: 0.9069 (mp) cc_final: 0.8605 (mt)
REVERT: C   69 TRP cc_start: 0.8906 (m100) cc_final: 0.8128 (m100)
REVERT: D   46 ARG cc_start: 0.7385 (mpt90) cc_final: 0.5666 (ttt180)
REVERT: E   29 ASN cc_start: 0.6881 (m110) cc_final: 0.6430 (m110)
REVERT: E   45 ILE cc_start: 0.8224 (mm) cc_final: 0.7902 (tp)
REVERT: F    3 HIS cc_start: 0.6935 (m170) cc_final: 0.6722 (m170)
REVERT: F   70 MET cc_start: 0.8554 (tpp) cc_final: 0.8209 (mmt)
REVERT: F   81 LYS cc_start: 0.7218 (ttpp) cc_final: 0.7017 (ttpt)
REVERT: F  108 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5663 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 323
  average time/residue: 0.1933
  time to fit residues: 82.9083
Evaluate side-chains
  223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 219
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 47 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A  68 GLN
B  34 ASN
C  29 ASN
C  38 GLN
D  34 ASN
D  87 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.128762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120684 restraints weight = 15553.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.122949 restraints weight = 8881.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124483 restraints weight = 5524.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   7830  Z= 0.321
  Angle     :  0.921  18.775  10626  Z= 0.466
  Chirality :  0.051   0.243   1182
  Planarity :  0.012   0.175   1392
  Dihedral  :  7.114  43.990   1056
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  2.43 %
    Allowed  : 12.13 %
    Favored  : 85.44 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.94 %
    Favored  : 93.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.27), residues: 948
  helix:  0.93 (0.37), residues: 198
  sheet: -0.25 (0.28), residues: 351
  loop : -3.61 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  69 
 HIS   0.006   0.001   HIS D   3 
 PHE   0.018   0.003   PHE E  71 
 TYR   0.037   0.002   TYR B 109 
 ARG   0.005   0.000   ARG D   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 272
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7060 (m110) cc_final: 0.6604 (m-40)
REVERT: A   85 ASP cc_start: 0.6561 (t0) cc_final: 0.5906 (t0)
REVERT: B   26 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5701 (pm20)
REVERT: B   40 TYR cc_start: 0.7378 (p90) cc_final: 0.7167 (p90)
REVERT: B   70 MET cc_start: 0.8239 (tpp) cc_final: 0.7856 (mtt)
REVERT: B   88 GLU cc_start: 0.8001 (tp30) cc_final: 0.7170 (tm-30)
REVERT: B   92 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7527 (mmtp)
REVERT: C   45 ILE cc_start: 0.9005 (mp) cc_final: 0.8759 (mt)
REVERT: C   46 ARG cc_start: 0.7215 (ttt180) cc_final: 0.4842 (ttp80)
REVERT: C   80 ASP cc_start: 0.7798 (t0) cc_final: 0.7386 (t0)
REVERT: D   23 GLN cc_start: 0.7840 (pm20) cc_final: 0.7540 (pm20)
REVERT: D   46 ARG cc_start: 0.7441 (mpt90) cc_final: 0.5468 (ttt180)
REVERT: D  134 ASP cc_start: 0.8353 (p0) cc_final: 0.8139 (p0)
REVERT: E    1 MET cc_start: 0.7393 (ttm) cc_final: 0.6524 (mtp)
REVERT: E   29 ASN cc_start: 0.6764 (m110) cc_final: 0.6480 (m-40)
REVERT: E  141 TYR cc_start: 0.7860 (m-10) cc_final: 0.7429 (m-80)
REVERT: F    3 HIS cc_start: 0.7431 (m170) cc_final: 0.7184 (m170)
REVERT: F    6 SER cc_start: 0.8561 (m) cc_final: 0.8325 (p)
REVERT: F  108 GLU cc_start: 0.6464 (mm-30) cc_final: 0.6055 (tp30)
REVERT: F  134 ASP cc_start: 0.8589 (p0) cc_final: 0.8176 (p0)
  outliers start: 5
  outliers final: 3
  residues processed: 276
  average time/residue: 0.1729
  time to fit residues: 65.2135
Evaluate side-chains
  210 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 206
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0870
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  89 GLN
C  29 ASN
D  89 GLN
E  68 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.132088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.124041 restraints weight = 15126.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.126318 restraints weight = 8446.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.127885 restraints weight = 5195.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   7830  Z= 0.238
  Angle     :  0.865  19.483  10626  Z= 0.428
  Chirality :  0.049   0.230   1182
  Planarity :  0.012   0.179   1392
  Dihedral  :  6.772  43.993   1056
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  2.53 %
    Allowed  : 12.55 %
    Favored  : 84.92 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.66 %
    Favored  : 94.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.28), residues: 948
  helix:  1.14 (0.37), residues: 198
  sheet:  0.30 (0.32), residues: 279
  loop : -3.03 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F  69 
 HIS   0.008   0.001   HIS B   3 
 PHE   0.014   0.002   PHE A 119 
 TYR   0.026   0.002   TYR B 109 
 ARG   0.008   0.000   ARG C   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 288
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8546 (ttt) cc_final: 0.8235 (ttt)
REVERT: A   29 ASN cc_start: 0.6748 (m110) cc_final: 0.6131 (m110)
REVERT: A   72 LEU cc_start: 0.8798 (tp) cc_final: 0.8585 (tt)
REVERT: A   74 LEU cc_start: 0.8960 (mp) cc_final: 0.8620 (mp)
REVERT: A   85 ASP cc_start: 0.7193 (t0) cc_final: 0.6797 (t0)
REVERT: A  126 MET cc_start: 0.8456 (mtp) cc_final: 0.8231 (mtp)
REVERT: B   17 LYS cc_start: 0.7045 (pttt) cc_final: 0.6666 (mmmt)
REVERT: B   40 TYR cc_start: 0.7133 (p90) cc_final: 0.6925 (p90)
REVERT: B   70 MET cc_start: 0.8246 (tpp) cc_final: 0.7810 (mtt)
REVERT: B   89 GLN cc_start: 0.7562 (tt0) cc_final: 0.7280 (tt0)
REVERT: C   29 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.6682 (m110)
REVERT: C   45 ILE cc_start: 0.8884 (mp) cc_final: 0.8642 (mt)
REVERT: C   80 ASP cc_start: 0.7786 (t0) cc_final: 0.7530 (t0)
REVERT: C   91 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6809 (tm-30)
REVERT: C  122 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7213 (mm-30)
REVERT: D   28 PHE cc_start: 0.8104 (p90) cc_final: 0.7398 (p90)
REVERT: D   29 ASN cc_start: 0.7896 (p0) cc_final: 0.7449 (p0)
REVERT: D   46 ARG cc_start: 0.7609 (mpt90) cc_final: 0.5229 (ttt180)
REVERT: D   47 GLU cc_start: 0.5911 (mp0) cc_final: 0.5565 (mp0)
REVERT: D   70 MET cc_start: 0.8500 (mmt) cc_final: 0.8151 (mmt)
REVERT: E    1 MET cc_start: 0.7159 (ttm) cc_final: 0.6908 (mtp)
REVERT: E  141 TYR cc_start: 0.7837 (m-10) cc_final: 0.7417 (m-80)
REVERT: F    4 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7858 (ttp80)
REVERT: F   26 GLU cc_start: 0.7223 (pt0) cc_final: 0.6364 (mm-30)
REVERT: F   70 MET cc_start: 0.9036 (tpp) cc_final: 0.8496 (tpp)
REVERT: F   82 GLU cc_start: 0.6807 (mp0) cc_final: 0.6592 (mp0)
REVERT: F   88 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: F  108 GLU cc_start: 0.6350 (mm-30) cc_final: 0.5867 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 291
  average time/residue: 0.1897
  time to fit residues: 74.5480
Evaluate side-chains
  239 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 237
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 16 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  38 GLN
C 147 ASN
D  68 GLN
F  29 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.121839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113870 restraints weight = 15882.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116116 restraints weight = 8911.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.117621 restraints weight = 5478.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   7830  Z= 0.339
  Angle     :  0.934  21.555  10626  Z= 0.461
  Chirality :  0.051   0.224   1182
  Planarity :  0.012   0.184   1392
  Dihedral  :  7.033  44.211   1056
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  2.53 %
    Allowed  : 12.97 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.90 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.28), residues: 948
  helix:  1.22 (0.37), residues: 198
  sheet:  0.20 (0.30), residues: 303
  loop : -3.43 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E  69 
 HIS   0.007   0.002   HIS F   3 
 PHE   0.023   0.003   PHE A  48 
 TYR   0.031   0.002   TYR D 109 
 ARG   0.005   0.001   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7287 (m110) cc_final: 0.6712 (m-40)
REVERT: A   45 ILE cc_start: 0.8599 (mp) cc_final: 0.8250 (mt)
REVERT: A   72 LEU cc_start: 0.8784 (tp) cc_final: 0.8530 (tt)
REVERT: B   17 LYS cc_start: 0.7393 (pttt) cc_final: 0.7086 (mmmt)
REVERT: B   40 TYR cc_start: 0.7614 (p90) cc_final: 0.7379 (p90)
REVERT: B   70 MET cc_start: 0.8368 (tpp) cc_final: 0.8055 (mtt)
REVERT: B   87 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7979 (mm-40)
REVERT: B   88 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7256 (tm-30)
REVERT: B   92 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7992 (mmtp)
REVERT: B  132 SER cc_start: 0.8344 (t) cc_final: 0.8088 (t)
REVERT: B  134 ASP cc_start: 0.8229 (p0) cc_final: 0.7768 (p0)
REVERT: C   20 ASP cc_start: 0.7655 (p0) cc_final: 0.7395 (p0)
REVERT: C   29 ASN cc_start: 0.7583 (m110) cc_final: 0.7156 (m-40)
REVERT: C   45 ILE cc_start: 0.9077 (mp) cc_final: 0.8705 (mt)
REVERT: C   50 TYR cc_start: 0.8809 (t80) cc_final: 0.8525 (t80)
REVERT: C  141 TYR cc_start: 0.7623 (m-10) cc_final: 0.7188 (m-10)
REVERT: D   28 PHE cc_start: 0.8306 (p90) cc_final: 0.7671 (p90)
REVERT: D   38 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7149 (mm-40)
REVERT: D   46 ARG cc_start: 0.7552 (mpt90) cc_final: 0.5281 (ttt180)
REVERT: D   82 GLU cc_start: 0.7890 (mp0) cc_final: 0.7648 (mp0)
REVERT: D   91 GLU cc_start: 0.7013 (pp20) cc_final: 0.6767 (pp20)
REVERT: E    2 ASP cc_start: 0.8220 (m-30) cc_final: 0.8010 (m-30)
REVERT: F   26 GLU cc_start: 0.7740 (pt0) cc_final: 0.6561 (mm-30)
REVERT: F   82 GLU cc_start: 0.6931 (mp0) cc_final: 0.6656 (mp0)
REVERT: F   88 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7304 (tm-30)
REVERT: F  150 VAL cc_start: 0.9409 (t) cc_final: 0.9198 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 261
  average time/residue: 0.1827
  time to fit residues: 64.4595
Evaluate side-chains
  196 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0980
   chunk 57 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 153 GLN
C  38 GLN
D  34 ASN
D  68 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.127392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.119037 restraints weight = 15264.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.121439 restraints weight = 8412.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.123018 restraints weight = 5132.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   7830  Z= 0.239
  Angle     :  0.852  21.185  10626  Z= 0.419
  Chirality :  0.048   0.214   1182
  Planarity :  0.012   0.184   1392
  Dihedral  :  6.743  45.960   1056
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  2.32 %
    Allowed  : 12.76 %
    Favored  : 84.92 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.15 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.28), residues: 948
  helix:  1.19 (0.37), residues: 198
  sheet:  0.02 (0.29), residues: 327
  loop : -3.32 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  69 
 HIS   0.007   0.001   HIS D   3 
 PHE   0.013   0.002   PHE A 119 
 TYR   0.021   0.002   TYR B 109 
 ARG   0.004   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7280 (m110) cc_final: 0.6679 (m-40)
REVERT: A   45 ILE cc_start: 0.8567 (mp) cc_final: 0.8232 (mt)
REVERT: A   72 LEU cc_start: 0.8733 (tp) cc_final: 0.8489 (tt)
REVERT: B    1 MET cc_start: 0.6388 (mpp) cc_final: 0.5953 (mpp)
REVERT: B   17 LYS cc_start: 0.7266 (ptmt) cc_final: 0.6878 (mmmt)
REVERT: B   40 TYR cc_start: 0.7518 (p90) cc_final: 0.7314 (p90)
REVERT: B   70 MET cc_start: 0.8343 (tpp) cc_final: 0.7953 (mtt)
REVERT: B   89 GLN cc_start: 0.8103 (tt0) cc_final: 0.7596 (tt0)
REVERT: B   92 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8037 (mmtm)
REVERT: B  132 SER cc_start: 0.8168 (t) cc_final: 0.7958 (t)
REVERT: C   29 ASN cc_start: 0.7402 (m110) cc_final: 0.7051 (m-40)
REVERT: C   45 ILE cc_start: 0.8976 (mp) cc_final: 0.8672 (mt)
REVERT: C   50 TYR cc_start: 0.8627 (t80) cc_final: 0.8346 (t80)
REVERT: C   70 MET cc_start: 0.8084 (mmm) cc_final: 0.7806 (mmt)
REVERT: C   80 ASP cc_start: 0.7882 (t0) cc_final: 0.7533 (t0)
REVERT: C   91 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: C  141 TYR cc_start: 0.7653 (m-10) cc_final: 0.7427 (m-10)
REVERT: D   28 PHE cc_start: 0.8071 (p90) cc_final: 0.7450 (p90)
REVERT: D   38 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7246 (mm-40)
REVERT: D   46 ARG cc_start: 0.7674 (mpt90) cc_final: 0.5108 (ttt180)
REVERT: D   87 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8462 (mm-40)
REVERT: D   91 GLU cc_start: 0.6918 (pp20) cc_final: 0.6580 (pp20)
REVERT: D  134 ASP cc_start: 0.8624 (p0) cc_final: 0.8306 (p0)
REVERT: E   45 ILE cc_start: 0.8499 (mt) cc_final: 0.8262 (mt)
REVERT: E   70 MET cc_start: 0.8436 (mmm) cc_final: 0.7951 (mmt)
REVERT: E   74 LEU cc_start: 0.8827 (mp) cc_final: 0.8151 (mt)
REVERT: F   26 GLU cc_start: 0.7680 (pt0) cc_final: 0.6374 (mm-30)
REVERT: F   70 MET cc_start: 0.9070 (tpp) cc_final: 0.8853 (mmt)
REVERT: F   82 GLU cc_start: 0.6919 (mp0) cc_final: 0.6658 (mp0)
REVERT: F   88 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7217 (tm-30)
REVERT: F  150 VAL cc_start: 0.9343 (t) cc_final: 0.9097 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 255
  average time/residue: 0.1677
  time to fit residues: 58.8762
Evaluate side-chains
  198 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 20 optimal weight:    0.0040
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9594

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.128271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120075 restraints weight = 15411.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.122413 restraints weight = 8665.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.123941 restraints weight = 5338.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   7830  Z= 0.236
  Angle     :  0.871  24.045  10626  Z= 0.421
  Chirality :  0.049   0.262   1182
  Planarity :  0.012   0.194   1392
  Dihedral  :  6.604  45.715   1056
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  2.22 %
    Allowed  : 12.55 %
    Favored  : 85.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.28), residues: 948
  helix:  1.26 (0.37), residues: 198
  sheet: -0.04 (0.29), residues: 315
  loop : -2.96 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  69 
 HIS   0.006   0.001   HIS B   3 
 PHE   0.014   0.002   PHE E  71 
 TYR   0.023   0.002   TYR F 109 
 ARG   0.003   0.000   ARG F 151 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7192 (m110) cc_final: 0.6635 (m110)
REVERT: A   72 LEU cc_start: 0.8779 (tp) cc_final: 0.8483 (tt)
REVERT: B   17 LYS cc_start: 0.7390 (ptmt) cc_final: 0.6952 (mmmt)
REVERT: B   45 ILE cc_start: 0.8380 (mp) cc_final: 0.8174 (mt)
REVERT: B   70 MET cc_start: 0.8370 (tpp) cc_final: 0.8101 (mtt)
REVERT: B   89 GLN cc_start: 0.7996 (tt0) cc_final: 0.7248 (tt0)
REVERT: B  132 SER cc_start: 0.8099 (t) cc_final: 0.7884 (t)
REVERT: C   45 ILE cc_start: 0.8952 (mp) cc_final: 0.8700 (mt)
REVERT: C   50 TYR cc_start: 0.8631 (t80) cc_final: 0.8232 (t80)
REVERT: C   70 MET cc_start: 0.7936 (mmm) cc_final: 0.7695 (mmt)
REVERT: C   80 ASP cc_start: 0.7818 (t0) cc_final: 0.7504 (t0)
REVERT: C   91 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7447 (tm-30)
REVERT: D   38 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7313 (mm110)
REVERT: D   46 ARG cc_start: 0.7511 (mpt90) cc_final: 0.5072 (ttt180)
REVERT: D   70 MET cc_start: 0.8410 (mmt) cc_final: 0.8038 (mmt)
REVERT: D   87 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8301 (mm-40)
REVERT: D   91 GLU cc_start: 0.6951 (pp20) cc_final: 0.6683 (pp20)
REVERT: D  132 SER cc_start: 0.8968 (m) cc_final: 0.8694 (p)
REVERT: D  134 ASP cc_start: 0.8583 (p0) cc_final: 0.8293 (p0)
REVERT: E    1 MET cc_start: 0.6546 (ttm) cc_final: 0.5931 (mtp)
REVERT: E    2 ASP cc_start: 0.8124 (m-30) cc_final: 0.7863 (m-30)
REVERT: E   70 MET cc_start: 0.8098 (mmm) cc_final: 0.7675 (mmt)
REVERT: F   26 GLU cc_start: 0.7602 (pt0) cc_final: 0.6371 (mm-30)
REVERT: F   70 MET cc_start: 0.9054 (tpp) cc_final: 0.8775 (mmt)
REVERT: F   82 GLU cc_start: 0.6760 (mp0) cc_final: 0.6547 (mp0)
REVERT: F   88 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: F  150 VAL cc_start: 0.9338 (t) cc_final: 0.9116 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1627
  time to fit residues: 56.8160
Evaluate side-chains
  200 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0020
   chunk 33 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B 115 ASN
C  38 GLN
E  23 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116344 restraints weight = 15515.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.118778 restraints weight = 8659.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120330 restraints weight = 5295.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7830  Z= 0.271
  Angle     :  0.858  17.709  10626  Z= 0.425
  Chirality :  0.049   0.199   1182
  Planarity :  0.011   0.175   1392
  Dihedral  :  6.757  48.395   1056
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  1.90 %
    Allowed  : 12.97 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.80 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.28), residues: 948
  helix:  1.26 (0.38), residues: 198
  sheet: -0.16 (0.29), residues: 315
  loop : -2.99 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  69 
 HIS   0.006   0.002   HIS D   3 
 PHE   0.019   0.002   PHE E  48 
 TYR   0.024   0.002   TYR F 109 
 ARG   0.003   0.000   ARG E   4 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7466 (m110) cc_final: 0.6884 (m-40)
REVERT: A   72 LEU cc_start: 0.8702 (tp) cc_final: 0.8459 (tt)
REVERT: B   17 LYS cc_start: 0.7419 (ptmt) cc_final: 0.7062 (mmmt)
REVERT: B   40 TYR cc_start: 0.7410 (p90) cc_final: 0.7118 (p90)
REVERT: B   70 MET cc_start: 0.8432 (tpp) cc_final: 0.7962 (mtt)
REVERT: B   89 GLN cc_start: 0.8009 (tt0) cc_final: 0.7546 (tt0)
REVERT: C   20 ASP cc_start: 0.7784 (p0) cc_final: 0.7457 (p0)
REVERT: C   45 ILE cc_start: 0.9010 (mp) cc_final: 0.8666 (mt)
REVERT: C   50 TYR cc_start: 0.8663 (t80) cc_final: 0.8462 (t80)
REVERT: C   80 ASP cc_start: 0.7755 (t0) cc_final: 0.7505 (t0)
REVERT: D   38 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7410 (mm110)
REVERT: D   46 ARG cc_start: 0.7577 (mpt90) cc_final: 0.5318 (ttt180)
REVERT: D   70 MET cc_start: 0.8453 (mmt) cc_final: 0.8087 (mmt)
REVERT: D   87 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8215 (mm-40)
REVERT: D   91 GLU cc_start: 0.7271 (pp20) cc_final: 0.6863 (pp20)
REVERT: D  132 SER cc_start: 0.9030 (m) cc_final: 0.8777 (p)
REVERT: D  134 ASP cc_start: 0.8603 (p0) cc_final: 0.8319 (p0)
REVERT: E    1 MET cc_start: 0.6359 (ttm) cc_final: 0.6024 (mtp)
REVERT: E    2 ASP cc_start: 0.8078 (m-30) cc_final: 0.7872 (m-30)
REVERT: E   70 MET cc_start: 0.7992 (mmm) cc_final: 0.7624 (mmt)
REVERT: E   91 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7035 (tm-30)
REVERT: F   70 MET cc_start: 0.9105 (tpp) cc_final: 0.8796 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1610
  time to fit residues: 54.0847
Evaluate side-chains
  193 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0870
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 GLN
C  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.119939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.111641 restraints weight = 16073.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114064 restraints weight = 8909.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.115687 restraints weight = 5426.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   7830  Z= 0.337
  Angle     :  0.953  30.429  10626  Z= 0.457
  Chirality :  0.051   0.223   1182
  Planarity :  0.012   0.209   1392
  Dihedral  :  7.113  51.880   1056
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  1.79 %
    Allowed  : 14.03 %
    Favored  : 84.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 948
  helix:  1.29 (0.37), residues: 201
  sheet: -0.36 (0.29), residues: 309
  loop : -3.10 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  69 
 HIS   0.006   0.001   HIS D   3 
 PHE   0.019   0.002   PHE E  48 
 TYR   0.026   0.002   TYR B 109 
 ARG   0.003   0.000   ARG C  14 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8684 (ttm) cc_final: 0.8467 (ttm)
REVERT: A   19 MET cc_start: 0.7870 (mtp) cc_final: 0.7584 (mtm)
REVERT: A   29 ASN cc_start: 0.7673 (m110) cc_final: 0.7046 (m-40)
REVERT: B    1 MET cc_start: 0.6630 (mpp) cc_final: 0.5649 (mpp)
REVERT: B   17 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7189 (mmmt)
REVERT: B   29 ASN cc_start: 0.6928 (p0) cc_final: 0.6598 (p0)
REVERT: B   40 TYR cc_start: 0.7660 (p90) cc_final: 0.7364 (p90)
REVERT: C   70 MET cc_start: 0.8046 (mmm) cc_final: 0.7660 (mmt)
REVERT: D   38 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7276 (mm110)
REVERT: D   46 ARG cc_start: 0.7722 (mpt90) cc_final: 0.5621 (ttt90)
REVERT: D   87 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8246 (mm-40)
REVERT: D  132 SER cc_start: 0.9156 (m) cc_final: 0.8781 (p)
REVERT: D  134 ASP cc_start: 0.8649 (p0) cc_final: 0.8366 (p0)
REVERT: E   20 ASP cc_start: 0.7656 (p0) cc_final: 0.6930 (p0)
REVERT: E   70 MET cc_start: 0.7969 (mmm) cc_final: 0.7751 (mmt)
REVERT: F   11 MET cc_start: 0.8591 (tpp) cc_final: 0.8288 (tpp)
REVERT: F   26 GLU cc_start: 0.7537 (pt0) cc_final: 0.6245 (mm-30)
REVERT: F   70 MET cc_start: 0.9114 (tpp) cc_final: 0.8793 (mmt)
REVERT: F   88 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7222 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1504
  time to fit residues: 52.7664
Evaluate side-chains
  188 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 86 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
C  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.126026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118174 restraints weight = 15742.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120479 restraints weight = 8722.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122013 restraints weight = 5297.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   7830  Z= 0.241
  Angle     :  0.876  23.658  10626  Z= 0.424
  Chirality :  0.049   0.228   1182
  Planarity :  0.012   0.191   1392
  Dihedral  :  6.796  49.807   1056
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  1.79 %
    Allowed  : 12.66 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.28), residues: 948
  helix:  1.16 (0.37), residues: 198
  sheet: -0.29 (0.29), residues: 315
  loop : -2.97 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  69 
 HIS   0.008   0.002   HIS D   3 
 PHE   0.030   0.002   PHE D  28 
 TYR   0.021   0.002   TYR F 109 
 ARG   0.003   0.000   ARG C  14 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7513 (m110) cc_final: 0.7018 (m-40)
REVERT: A   45 ILE cc_start: 0.8694 (mp) cc_final: 0.8489 (mt)
REVERT: A   72 LEU cc_start: 0.8658 (tp) cc_final: 0.8426 (tt)
REVERT: A   99 THR cc_start: 0.9092 (t) cc_final: 0.8683 (t)
REVERT: B   17 LYS cc_start: 0.7567 (ptmt) cc_final: 0.7070 (mmmt)
REVERT: B   23 GLN cc_start: 0.8303 (pm20) cc_final: 0.7496 (tt0)
REVERT: B   40 TYR cc_start: 0.7579 (p90) cc_final: 0.7250 (p90)
REVERT: C   45 ILE cc_start: 0.9012 (mp) cc_final: 0.8594 (mt)
REVERT: C   70 MET cc_start: 0.7980 (mmm) cc_final: 0.7617 (mmt)
REVERT: C   80 ASP cc_start: 0.7781 (t0) cc_final: 0.7563 (t0)
REVERT: C   91 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7245 (tm-30)
REVERT: D   38 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7288 (mm-40)
REVERT: D   46 ARG cc_start: 0.7738 (mpt90) cc_final: 0.5539 (ttt90)
REVERT: D   87 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8101 (mm-40)
REVERT: D   91 GLU cc_start: 0.7106 (pp20) cc_final: 0.6866 (pp20)
REVERT: E   20 ASP cc_start: 0.7842 (p0) cc_final: 0.7178 (p0)
REVERT: E   70 MET cc_start: 0.8014 (mmm) cc_final: 0.7586 (mmt)
REVERT: E   92 LYS cc_start: 0.7184 (mmtp) cc_final: 0.6755 (mmtm)
REVERT: F   11 MET cc_start: 0.8488 (tpp) cc_final: 0.8184 (tpp)
REVERT: F   26 GLU cc_start: 0.7396 (pt0) cc_final: 0.6360 (mm-30)
REVERT: F   70 MET cc_start: 0.9027 (tpp) cc_final: 0.8712 (tpp)
REVERT: F   82 GLU cc_start: 0.7295 (mp0) cc_final: 0.7052 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1556
  time to fit residues: 56.5962
Evaluate side-chains
  193 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0970
   chunk 18 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
E 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.121169 restraints weight = 15674.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.123462 restraints weight = 8632.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.124992 restraints weight = 5239.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   7830  Z= 0.232
  Angle     :  0.863  21.828  10626  Z= 0.418
  Chirality :  0.049   0.227   1182
  Planarity :  0.012   0.185   1392
  Dihedral  :  6.556  50.567   1056
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  1.69 %
    Allowed  : 13.29 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.28), residues: 948
  helix:  1.13 (0.37), residues: 198
  sheet: -0.15 (0.30), residues: 315
  loop : -2.91 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  69 
 HIS   0.009   0.002   HIS D   3 
 PHE   0.037   0.002   PHE D  28 
 TYR   0.020   0.001   TYR B 109 
 ARG   0.003   0.000   ARG B  14 

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7469 (m110) cc_final: 0.7027 (m-40)
REVERT: A   72 LEU cc_start: 0.8683 (tp) cc_final: 0.8445 (tt)
REVERT: A   74 LEU cc_start: 0.8946 (mp) cc_final: 0.8708 (mp)
REVERT: A  109 TYR cc_start: 0.7277 (m-80) cc_final: 0.6609 (m-10)
REVERT: B    1 MET cc_start: 0.6456 (mpp) cc_final: 0.6077 (mpp)
REVERT: B   17 LYS cc_start: 0.7542 (ptmt) cc_final: 0.7048 (mmmt)
REVERT: B   23 GLN cc_start: 0.8269 (pm20) cc_final: 0.7544 (tt0)
REVERT: B   40 TYR cc_start: 0.7373 (p90) cc_final: 0.7077 (p90)
REVERT: B   92 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8007 (mttp)
REVERT: C   45 ILE cc_start: 0.9040 (mp) cc_final: 0.8777 (mt)
REVERT: C   70 MET cc_start: 0.7965 (mmm) cc_final: 0.7550 (mmt)
REVERT: C   91 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: D   38 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7269 (mm-40)
REVERT: D   70 MET cc_start: 0.8509 (mmt) cc_final: 0.8219 (mmt)
REVERT: D   87 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7898 (mm-40)
REVERT: E    1 MET cc_start: 0.6310 (mtp) cc_final: 0.6099 (mtp)
REVERT: E   20 ASP cc_start: 0.7624 (p0) cc_final: 0.6887 (p0)
REVERT: E   45 ILE cc_start: 0.8469 (mt) cc_final: 0.8210 (mt)
REVERT: E   59 THR cc_start: 0.8650 (p) cc_final: 0.8438 (m)
REVERT: E   70 MET cc_start: 0.8003 (mmm) cc_final: 0.7546 (mmt)
REVERT: E   99 THR cc_start: 0.8680 (t) cc_final: 0.8470 (p)
REVERT: F   11 MET cc_start: 0.8523 (tpp) cc_final: 0.8254 (tpp)
REVERT: F   26 GLU cc_start: 0.7196 (pt0) cc_final: 0.6408 (mm-30)
REVERT: F   70 MET cc_start: 0.9010 (tpp) cc_final: 0.8729 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1607
  time to fit residues: 58.6091
Evaluate side-chains
  206 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112869 restraints weight = 15822.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.115116 restraints weight = 8791.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116555 restraints weight = 5395.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.5601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   7830  Z= 0.341
  Angle     :  0.934  21.004  10626  Z= 0.460
  Chirality :  0.051   0.209   1182
  Planarity :  0.012   0.182   1392
  Dihedral  :  6.990  51.858   1056
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  1.69 %
    Allowed  : 13.82 %
    Favored  : 84.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.11 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.28), residues: 948
  helix:  1.26 (0.37), residues: 198
  sheet: -0.34 (0.30), residues: 309
  loop : -3.05 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  69 
 HIS   0.007   0.001   HIS D   3 
 PHE   0.035   0.003   PHE D  28 
 TYR   0.028   0.002   TYR F 109 
 ARG   0.004   0.000   ARG E   4 

===============================================================================
Job complete
usr+sys time: 2371.43 seconds
wall clock time: 42 minutes 8.20 seconds (2528.20 seconds total)