Starting phenix.real_space_refine
on Tue Mar  3 13:26:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sax_24958/03_2026/7sax_24958.map"
  }
  resolution = 3.0
  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=   0.005
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      28      5.16       5
     C    3431      2.51       5
     N     882      2.21       5
     O     964      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 5305
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1627
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
    Chain: "B"
      Number of atoms: 1614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1614
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
    Chain: "C"
      Number of atoms: 473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 473
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 1, 'TRANS': 58}
    Chain: "D"
      Number of atoms: 430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 430
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
    Chain: "E"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'TRANS': 49}
    Chain: "F"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'TRANS': 49}
    Chain: "G"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'TRANS': 49}
  Time building chain proxies: 1.38, per 1000 atoms: 0.26
  Number of scatterers: 5305
  At special positions: 0
  Unit cell: (66.56, 58.24, 129.792, 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      28     16.00
     O     964      8.00
     N     882      7.00
     C    3431      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: 0.40
  Conformation dependent library (CDL) restraints added in 383.9 milliseconds
  

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1232

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 25
      removed outlier: 3.823A  pdb=" N   ALA A  25 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 69
      removed outlier: 5.074A  pdb=" N   LEU A  66 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LYS A  67 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   GLU A  68 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASN A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 104
      Proline residue:  A  75  - end of helix
      removed outlier: 3.592A  pdb=" N   VAL A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 128
    Processing helix  chain 'A' and resid 132 through 153
      removed outlier: 3.690A  pdb=" N   GLU A 136 " --> pdb=" O   GLY A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 181
    Processing helix  chain 'A' and resid 185 through 215
      removed outlier: 4.253A  pdb=" N   MET A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 28
      removed outlier: 5.295A  pdb=" N   LEU B  18 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL B  19 " --> pdb=" O   ILE B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 63
    Processing helix  chain 'B' and resid 69 through 104
      Proline residue:  B  75  - end of helix
      removed outlier: 3.716A  pdb=" N   LEU B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 128
    Processing helix  chain 'B' and resid 132 through 153
      removed outlier: 3.519A  pdb=" N   LEU B 151 " --> pdb=" O   GLU B 147 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 180
    Processing helix  chain 'B' and resid 185 through 214
    Processing helix  chain 'C' and resid 10 through 31
      removed outlier: 4.013A  pdb=" N   LEU C  14 " --> pdb=" O   GLY C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 58
      removed outlier: 3.869A  pdb=" N   ILE C  40 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLY C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 31
      removed outlier: 3.804A  pdb=" N   LEU D  14 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 55
      removed outlier: 4.277A  pdb=" N   MET D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY D  55 " --> pdb=" O   PHE D  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 31
      removed outlier: 3.750A  pdb=" N   LEU E  14 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 54
      removed outlier: 3.899A  pdb=" N   GLY E  41 " --> pdb=" O   GLU E  37 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 57
      No H-bonds generated for 'chain 'E' and resid 55 through 57'
    Processing helix  chain 'F' and resid 10 through 31
      removed outlier: 4.125A  pdb=" N   LEU F  14 " --> pdb=" O   GLY F  10 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE F  15 " --> pdb=" O   ILE F  11 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA F  19 " --> pdb=" O   ILE F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 55
    Processing helix  chain 'G' and resid 10 through 31
      removed outlier: 4.011A  pdb=" N   LEU G  14 " --> pdb=" O   GLY G  10 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA G  19 " --> pdb=" O   ILE G  15 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 55
      removed outlier: 4.193A  pdb=" N   MET G  39 " --> pdb=" O   GLY G  35 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY G  41 " --> pdb=" O   GLU G  37 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1215 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: 0.72

  Time building geometry restraints manager: 0.55 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: 1709
        1.34 -     1.46: 681
        1.46 -     1.57: 2938
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 5384
  Sorted by residual:
  bond pdb=" CG1 ILE D  15 "
       pdb=" CD1 ILE D  15 "
    ideal  model  delta    sigma   weight residual
    1.513  1.428  0.085 3.90e-02 6.57e+02 4.74e+00
  bond pdb=" CB  MET A  12 "
       pdb=" CG  MET A  12 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.60e+00
  bond pdb=" CB  MET E  54 "
       pdb=" CG  MET E  54 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.33e+00
  bond pdb=" CG1 ILE B  15 "
       pdb=" CD1 ILE B  15 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.28e+00
  bond pdb=" CG1 ILE D  23 "
       pdb=" CD1 ILE D  23 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.26e+00
  ... (remaining 5379 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 7162
        2.35 -     4.71: 81
        4.71 -     7.06: 10
        7.06 -     9.41: 1
        9.41 -    11.76: 1
  Bond angle restraints: 7255
  Sorted by residual:
  angle pdb=" CB  MET D  54 "
        pdb=" CG  MET D  54 "
        pdb=" SD  MET D  54 "
      ideal   model   delta    sigma   weight residual
     112.70  100.94   11.76 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" C   ILE E  53 "
        pdb=" N   MET E  54 "
        pdb=" CA  MET E  54 "
      ideal   model   delta    sigma   weight residual
     122.31  115.73    6.58 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" CB  MET E  54 "
        pdb=" CG  MET E  54 "
        pdb=" SD  MET E  54 "
      ideal   model   delta    sigma   weight residual
     112.70  103.40    9.30 3.00e+00 1.11e-01 9.62e+00
  angle pdb=" C   ARG A  11 "
        pdb=" N   MET A  12 "
        pdb=" CA  MET A  12 "
      ideal   model   delta    sigma   weight residual
     122.06  116.31    5.75 1.86e+00 2.89e-01 9.55e+00
  angle pdb=" CA  ARG A   9 "
        pdb=" CB  ARG A   9 "
        pdb=" CG  ARG A   9 "
      ideal   model   delta    sigma   weight residual
     114.10  118.91   -4.81 2.00e+00 2.50e-01 5.79e+00
  ... (remaining 7250 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 2882
       17.57 -    35.14: 267
       35.14 -    52.71: 38
       52.71 -    70.28: 8
       70.28 -    87.85: 2
  Dihedral angle restraints: 3197
    sinusoidal: 1279
      harmonic: 1918
  Sorted by residual:
  dihedral pdb=" CA  MET E  54 "
           pdb=" C   MET E  54 "
           pdb=" N   GLY E  55 "
           pdb=" CA  GLY E  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.94   22.06     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  VAL A 115 "
           pdb=" C   VAL A 115 "
           pdb=" N   LYS A 116 "
           pdb=" CA  LYS A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.41   18.59     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  MET A  12 "
           pdb=" C   MET A  12 "
           pdb=" N   ILE A  13 "
           pdb=" CA  ILE A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.76   18.24     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3194 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 589
       0.043 -    0.086: 234
       0.086 -    0.130: 24
       0.130 -    0.173: 5
       0.173 -    0.216: 2
  Chirality restraints: 854
  Sorted by residual:
  chirality pdb=" CB  VAL F  22 "
            pdb=" CA  VAL F  22 "
            pdb=" CG1 VAL F  22 "
            pdb=" CG2 VAL F  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE B 156 "
            pdb=" CA  ILE B 156 "
            pdb=" CG1 ILE B 156 "
            pdb=" CG2 ILE B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality pdb=" CA  MET E  54 "
            pdb=" N   MET E  54 "
            pdb=" C   MET E  54 "
            pdb=" CB  MET E  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 851 not shown)

  Planarity restraints: 908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  52 "    0.011 2.00e-02 2.50e+03   1.13e-02 2.24e+00
        pdb=" CG  PHE C  52 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  52 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  52 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  52 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  52 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  12 "    0.006 2.00e-02 2.50e+03   1.18e-02 1.40e+00
        pdb=" C   MET A  12 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   MET A  12 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ILE A  13 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A   9 "    0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   ARG A   9 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   ARG A   9 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLN A  10 "    0.006 2.00e-02 2.50e+03
  ... (remaining 905 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 234
        2.72 -     3.26: 5640
        3.26 -     3.81: 8814
        3.81 -     4.35: 10573
        4.35 -     4.90: 18257
  Nonbonded interactions: 43518
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B   9 "
            pdb=" OE2 GLU C  47 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" O   ALA B  60 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" NE2 GLN A  51 "
            pdb=" OD1 ASP A  55 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG1 THR A 112 "
            pdb=" OD1 ASP A 114 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE1 GLU A 131 "
            pdb=" NH1 ARG A 133 "
     model   vdw
     2.283 3.120
  ... (remaining 43513 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' and resid 5 through 215)
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 9 through 60)
  selection = (chain 'D' and resid 9 through 60)
}
ncs_group {
  reference = (chain 'E' and resid 9 through 57)
  selection = (chain 'F' and resid 9 through 57)
  selection = (chain 'G' and resid 9 through 57)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.730
  Find NCS groups from input model:        0.070
  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:6.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
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      :  0.007   0.085   5384  Z= 0.300
  Angle     :  0.660  11.764   7255  Z= 0.344
  Chirality :  0.044   0.216    854
  Planarity :  0.003   0.018    908
  Dihedral  : 13.544  87.846   1965
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.22 (0.33), residues: 675
  helix:  1.69 (0.23), residues: 507
  sheet:  None (None), residues: 0
  loop : -2.01 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A   9 
 TYR   0.017   0.003   TYR A 117 
 PHE   0.026   0.002   PHE C  52 
 TRP   0.009   0.001   TRP G  38 
 HIS   0.002   0.001   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00739 ( 5384)
  covalent geometry    : angle       0.66008 ( 7255)
  hydrogen bonds       : bond        0.13364 (  405)
  hydrogen bonds       : angle       5.16921 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7621 (pt0) cc_final: 0.7325 (pt0)
REVERT: A   10 GLN cc_start: 0.7704 (mt0) cc_final: 0.7308 (mt0)
REVERT: A   88 GLN cc_start: 0.7893 (tp40) cc_final: 0.7247 (tm-30)
REVERT: A   96 GLU cc_start: 0.7158 (pt0) cc_final: 0.6717 (mt-10)
REVERT: B   34 ASP cc_start: 0.7712 (m-30) cc_final: 0.7494 (m-30)
REVERT: B   62 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7042 (mmt-90)
REVERT: B  147 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6974 (mt-10)
REVERT: B  194 GLU cc_start: 0.7372 (tp30) cc_final: 0.6803 (tp30)
REVERT: B  205 SER cc_start: 0.8607 (p) cc_final: 0.8398 (p)
REVERT: C   37 GLU cc_start: 0.7341 (mp0) cc_final: 0.7128 (mp0)
REVERT: C   54 MET cc_start: 0.7212 (mmm) cc_final: 0.6882 (mmm)
REVERT: D    6 LYS cc_start: 0.5783 (ptpp) cc_final: 0.5258 (ptmt)
REVERT: F   34 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7592 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.5484
  time to fit residues: 83.4364
Evaluate side-chains
  122 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.139030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.110816 restraints weight = 6199.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.68
r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5384  Z= 0.109
  Angle     :  0.461   5.748   7255  Z= 0.245
  Chirality :  0.036   0.152    854
  Planarity :  0.003   0.016    908
  Dihedral  :  3.953  15.375    705
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 12.39 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.32 (0.33), residues: 675
  helix:  2.48 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.72 (0.49), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  11 
 TYR   0.009   0.002   TYR A 117 
 PHE   0.017   0.001   PHE A  61 
 TRP   0.010   0.001   TRP G  38 
 HIS   0.011   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5384)
  covalent geometry    : angle       0.46082 ( 7255)
  hydrogen bonds       : bond        0.03642 (  405)
  hydrogen bonds       : angle       3.78242 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7693 (pt0) cc_final: 0.7455 (pt0)
REVERT: A   88 GLN cc_start: 0.8289 (tp40) cc_final: 0.7717 (tm-30)
REVERT: A  139 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7355 (pt0)
REVERT: A  163 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: B  194 GLU cc_start: 0.8079 (tp30) cc_final: 0.7607 (tp30)
REVERT: B  209 LYS cc_start: 0.8304 (tttp) cc_final: 0.8045 (ttpm)
REVERT: C   54 MET cc_start: 0.7788 (mmm) cc_final: 0.7473 (mmm)
REVERT: D    6 LYS cc_start: 0.5586 (ptpp) cc_final: 0.4944 (ptmt)
REVERT: D   38 TRP cc_start: 0.7666 (t60) cc_final: 0.7026 (t60)
REVERT: F   34 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7611 (tppt)
  outliers start: 22
  outliers final: 6
  residues processed: 134
  average time/residue: 0.5046
  time to fit residues: 70.5460
Evaluate side-chains
  129 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
B  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.138335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.110261 restraints weight = 6244.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.69
r_work: 0.3084 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5384  Z= 0.121
  Angle     :  0.464   6.910   7255  Z= 0.246
  Chirality :  0.037   0.150    854
  Planarity :  0.002   0.019    908
  Dihedral  :  3.848  14.338    705
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.80 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.51 (0.33), residues: 675
  helix:  2.68 (0.22), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.90 (0.46), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  62 
 TYR   0.010   0.002   TYR B  17 
 PHE   0.026   0.001   PHE C  52 
 TRP   0.009   0.001   TRP G  38 
 HIS   0.008   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5384)
  covalent geometry    : angle       0.46445 ( 7255)
  hydrogen bonds       : bond        0.03551 (  405)
  hydrogen bonds       : angle       3.60983 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   10 GLN cc_start: 0.7725 (mt0) cc_final: 0.7505 (mt0)
REVERT: A   88 GLN cc_start: 0.8228 (tp40) cc_final: 0.7573 (tm-30)
REVERT: A  163 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7354 (mm-30)
REVERT: B   63 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6541 (pm20)
REVERT: B  194 GLU cc_start: 0.8109 (tp30) cc_final: 0.7604 (tp30)
REVERT: B  209 LYS cc_start: 0.8374 (tttp) cc_final: 0.8076 (ttpm)
REVERT: C   54 MET cc_start: 0.7704 (mmm) cc_final: 0.7455 (mmm)
REVERT: D    6 LYS cc_start: 0.5547 (ptpp) cc_final: 0.4903 (ptmt)
  outliers start: 22
  outliers final: 6
  residues processed: 129
  average time/residue: 0.5240
  time to fit residues: 70.3736
Evaluate side-chains
  124 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0470
   chunk 35 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.139924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.112004 restraints weight = 6249.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.71
r_work: 0.3112 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5384  Z= 0.104
  Angle     :  0.450   6.880   7255  Z= 0.236
  Chirality :  0.036   0.140    854
  Planarity :  0.002   0.021    908
  Dihedral  :  3.678  14.402    705
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 16.52 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.75 (0.33), residues: 675
  helix:  2.85 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.82 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  62 
 TYR   0.009   0.002   TYR B  17 
 PHE   0.027   0.001   PHE C  52 
 TRP   0.011   0.001   TRP G  38 
 HIS   0.006   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5384)
  covalent geometry    : angle       0.44950 ( 7255)
  hydrogen bonds       : bond        0.03257 (  405)
  hydrogen bonds       : angle       3.45157 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   10 GLN cc_start: 0.7719 (mt0) cc_final: 0.7451 (mt0)
REVERT: A   88 GLN cc_start: 0.8231 (tp40) cc_final: 0.7678 (tm-30)
REVERT: A  156 ILE cc_start: 0.7116 (tp) cc_final: 0.6746 (tt)
REVERT: A  163 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: B   63 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6494 (pm20)
REVERT: B   99 THR cc_start: 0.8352 (t) cc_final: 0.8061 (p)
REVERT: B  194 GLU cc_start: 0.8108 (tp30) cc_final: 0.7605 (tp30)
REVERT: B  209 LYS cc_start: 0.8430 (tttp) cc_final: 0.8090 (ttpm)
REVERT: C   54 MET cc_start: 0.7692 (mmm) cc_final: 0.7357 (mmm)
REVERT: C   56 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6580 (t80)
REVERT: C   57 MET cc_start: 0.6928 (mmp) cc_final: 0.6711 (ttm)
REVERT: D    6 LYS cc_start: 0.5534 (ptpp) cc_final: 0.4872 (ptmt)
REVERT: E   47 GLU cc_start: 0.7685 (tp30) cc_final: 0.7200 (tp30)
  outliers start: 25
  outliers final: 9
  residues processed: 131
  average time/residue: 0.4636
  time to fit residues: 63.4223
Evaluate side-chains
  131 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.137614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109154 restraints weight = 6325.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.74
r_work: 0.3101 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   5384  Z= 0.110
  Angle     :  0.456   6.552   7255  Z= 0.242
  Chirality :  0.036   0.124    854
  Planarity :  0.002   0.017    908
  Dihedral  :  3.651  14.550    705
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 18.31 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.82 (0.33), residues: 675
  helix:  2.90 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.79 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  62 
 TYR   0.012   0.002   TYR B  17 
 PHE   0.011   0.001   PHE A  61 
 TRP   0.012   0.001   TRP G  38 
 HIS   0.010   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5384)
  covalent geometry    : angle       0.45612 ( 7255)
  hydrogen bonds       : bond        0.03309 (  405)
  hydrogen bonds       : angle       3.45666 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7634 (pt0) cc_final: 0.7368 (pt0)
REVERT: A   10 GLN cc_start: 0.7746 (mt0) cc_final: 0.7491 (mt0)
REVERT: A   88 GLN cc_start: 0.8216 (tp40) cc_final: 0.7597 (tm-30)
REVERT: A  156 ILE cc_start: 0.7169 (tp) cc_final: 0.6850 (tt)
REVERT: A  163 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7465 (mm-30)
REVERT: B   63 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6500 (pm20)
REVERT: B   99 THR cc_start: 0.8355 (t) cc_final: 0.8060 (p)
REVERT: B  194 GLU cc_start: 0.8142 (tp30) cc_final: 0.7683 (tp30)
REVERT: B  209 LYS cc_start: 0.8454 (tttp) cc_final: 0.8170 (ttpt)
REVERT: C   57 MET cc_start: 0.6946 (mmp) cc_final: 0.6723 (ttm)
REVERT: D    6 LYS cc_start: 0.5495 (ptpp) cc_final: 0.4814 (ptmt)
REVERT: E   47 GLU cc_start: 0.7745 (tp30) cc_final: 0.7253 (tp30)
  outliers start: 23
  outliers final: 9
  residues processed: 129
  average time/residue: 0.4953
  time to fit residues: 66.6327
Evaluate side-chains
  129 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
B  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.139639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.111535 restraints weight = 6293.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.71
r_work: 0.3105 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5384  Z= 0.112
  Angle     :  0.458   6.538   7255  Z= 0.242
  Chirality :  0.036   0.126    854
  Planarity :  0.002   0.016    908
  Dihedral  :  3.642  14.741    705
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 18.31 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.83 (0.33), residues: 675
  helix:  2.91 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.79 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  62 
 TYR   0.011   0.002   TYR B  17 
 PHE   0.027   0.001   PHE C  52 
 TRP   0.013   0.001   TRP G  38 
 HIS   0.008   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5384)
  covalent geometry    : angle       0.45843 ( 7255)
  hydrogen bonds       : bond        0.03314 (  405)
  hydrogen bonds       : angle       3.45604 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7546 (pt0) cc_final: 0.7283 (pt0)
REVERT: A   10 GLN cc_start: 0.7755 (mt0) cc_final: 0.7513 (mt0)
REVERT: A   88 GLN cc_start: 0.8188 (tp40) cc_final: 0.7576 (tm-30)
REVERT: A  156 ILE cc_start: 0.7196 (tp) cc_final: 0.6859 (tt)
REVERT: A  163 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7436 (mm-30)
REVERT: B   63 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6411 (pm20)
REVERT: B   99 THR cc_start: 0.8358 (t) cc_final: 0.8069 (p)
REVERT: B  194 GLU cc_start: 0.8157 (tp30) cc_final: 0.7705 (tp30)
REVERT: B  209 LYS cc_start: 0.8451 (tttp) cc_final: 0.8173 (ttpt)
REVERT: D    6 LYS cc_start: 0.5450 (ptpp) cc_final: 0.4832 (ptmt)
REVERT: E   47 GLU cc_start: 0.7760 (tp30) cc_final: 0.7277 (tp30)
  outliers start: 26
  outliers final: 14
  residues processed: 136
  average time/residue: 0.5070
  time to fit residues: 72.0914
Evaluate side-chains
  135 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain F residue   27 MET
Chi-restraints excluded: chain G residue   37 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
B  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.138033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109603 restraints weight = 6324.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.73
r_work: 0.3068 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5384  Z= 0.115
  Angle     :  0.470   6.623   7255  Z= 0.250
  Chirality :  0.037   0.132    854
  Planarity :  0.002   0.016    908
  Dihedral  :  3.663  14.815    705
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.11 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.83 (0.33), residues: 675
  helix:  2.87 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.76 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  62 
 TYR   0.013   0.002   TYR B  17 
 PHE   0.011   0.001   PHE A  61 
 TRP   0.015   0.001   TRP G  38 
 HIS   0.010   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5384)
  covalent geometry    : angle       0.46989 ( 7255)
  hydrogen bonds       : bond        0.03349 (  405)
  hydrogen bonds       : angle       3.45794 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7563 (pt0) cc_final: 0.7293 (pt0)
REVERT: A   10 GLN cc_start: 0.7730 (mt0) cc_final: 0.7509 (mt0)
REVERT: A   88 GLN cc_start: 0.8186 (tp40) cc_final: 0.7565 (tm-30)
REVERT: A   96 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7430 (mt-10)
REVERT: A  156 ILE cc_start: 0.7202 (tp) cc_final: 0.6887 (tt)
REVERT: A  163 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7436 (mm-30)
REVERT: B   63 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6406 (pm20)
REVERT: B   99 THR cc_start: 0.8363 (t) cc_final: 0.8064 (p)
REVERT: B  194 GLU cc_start: 0.8135 (tp30) cc_final: 0.7681 (tp30)
REVERT: B  209 LYS cc_start: 0.8410 (tttp) cc_final: 0.8123 (ttpt)
REVERT: D    6 LYS cc_start: 0.5347 (ptpp) cc_final: 0.4733 (ptmt)
REVERT: D   39 MET cc_start: 0.8626 (mtm) cc_final: 0.8317 (mtp)
REVERT: E   47 GLU cc_start: 0.7776 (tp30) cc_final: 0.7297 (tp30)
  outliers start: 22
  outliers final: 14
  residues processed: 129
  average time/residue: 0.5354
  time to fit residues: 72.0218
Evaluate side-chains
  134 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain D residue   30 ILE
Chi-restraints excluded: chain F residue   27 MET
Chi-restraints excluded: chain G residue   37 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.137059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.108433 restraints weight = 6345.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.74
r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5384  Z= 0.112
  Angle     :  0.469   6.924   7255  Z= 0.249
  Chirality :  0.037   0.131    854
  Planarity :  0.002   0.016    908
  Dihedral  :  3.643  14.760    705
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 20.47 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.89 (0.33), residues: 675
  helix:  2.92 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.73 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  62 
 TYR   0.013   0.002   TYR B  17 
 PHE   0.028   0.001   PHE C  52 
 TRP   0.018   0.001   TRP G  38 
 HIS   0.009   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5384)
  covalent geometry    : angle       0.46891 ( 7255)
  hydrogen bonds       : bond        0.03310 (  405)
  hydrogen bonds       : angle       3.44360 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7535 (pt0) cc_final: 0.7250 (pt0)
REVERT: A   10 GLN cc_start: 0.7738 (mt0) cc_final: 0.7510 (mt0)
REVERT: A   88 GLN cc_start: 0.8190 (tp40) cc_final: 0.7559 (tm-30)
REVERT: A   96 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7440 (mt-10)
REVERT: A  156 ILE cc_start: 0.7203 (tp) cc_final: 0.6865 (tt)
REVERT: B   63 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6327 (pm20)
REVERT: B   99 THR cc_start: 0.8376 (t) cc_final: 0.8080 (p)
REVERT: B  147 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7599 (mt-10)
REVERT: B  194 GLU cc_start: 0.8155 (tp30) cc_final: 0.7707 (tp30)
REVERT: B  209 LYS cc_start: 0.8462 (tttp) cc_final: 0.8187 (ttpp)
REVERT: C   54 MET cc_start: 0.7702 (mmm) cc_final: 0.7234 (mmm)
REVERT: D    6 LYS cc_start: 0.5276 (ptpp) cc_final: 0.4678 (ptmt)
REVERT: E   47 GLU cc_start: 0.7771 (tp30) cc_final: 0.7297 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 133
  average time/residue: 0.5321
  time to fit residues: 73.8468
Evaluate side-chains
  138 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain D residue   30 ILE
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0770
   chunk 5 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.3742

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
B  44 ASN
B  74 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.137130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.109008 restraints weight = 6391.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.72
r_work: 0.3026 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5384  Z= 0.144
  Angle     :  0.505   6.686   7255  Z= 0.267
  Chirality :  0.038   0.138    854
  Planarity :  0.002   0.016    908
  Dihedral  :  3.810  15.862    705
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.83 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.82 (0.33), residues: 675
  helix:  2.86 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.76 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  62 
 TYR   0.014   0.003   TYR B  17 
 PHE   0.025   0.001   PHE C  52 
 TRP   0.018   0.001   TRP G  38 
 HIS   0.010   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5384)
  covalent geometry    : angle       0.50507 ( 7255)
  hydrogen bonds       : bond        0.03620 (  405)
  hydrogen bonds       : angle       3.54835 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7721 (pt0) cc_final: 0.7413 (pt0)
REVERT: A   88 GLN cc_start: 0.8158 (tp40) cc_final: 0.7579 (tm-30)
REVERT: A   96 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7392 (mt-10)
REVERT: A  156 ILE cc_start: 0.7199 (tp) cc_final: 0.6877 (tt)
REVERT: B   63 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6461 (pm20)
REVERT: B   99 THR cc_start: 0.8439 (t) cc_final: 0.8130 (p)
REVERT: B  147 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7594 (mt-10)
REVERT: B  194 GLU cc_start: 0.8144 (tp30) cc_final: 0.7690 (tp30)
REVERT: B  209 LYS cc_start: 0.8402 (tttp) cc_final: 0.8132 (ttpt)
REVERT: C   54 MET cc_start: 0.7666 (mmm) cc_final: 0.7204 (mmm)
REVERT: D    6 LYS cc_start: 0.5501 (ptpp) cc_final: 0.4858 (ptmt)
REVERT: E   47 GLU cc_start: 0.7801 (tp30) cc_final: 0.7305 (tp30)
REVERT: F   34 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7620 (ttpt)
  outliers start: 22
  outliers final: 13
  residues processed: 136
  average time/residue: 0.5276
  time to fit residues: 74.8510
Evaluate side-chains
  135 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain D residue   30 ILE
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.138954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.110676 restraints weight = 6350.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.72
r_work: 0.3058 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5384  Z= 0.116
  Angle     :  0.487   7.562   7255  Z= 0.257
  Chirality :  0.037   0.135    854
  Planarity :  0.002   0.017    908
  Dihedral  :  3.723  16.603    705
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.26 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.92 (0.33), residues: 675
  helix:  2.93 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.71 (0.49), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  62 
 TYR   0.012   0.002   TYR B  17 
 PHE   0.027   0.001   PHE C  52 
 TRP   0.020   0.001   TRP G  38 
 HIS   0.009   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5384)
  covalent geometry    : angle       0.48665 ( 7255)
  hydrogen bonds       : bond        0.03396 (  405)
  hydrogen bonds       : angle       3.48952 ( 1215)

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

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

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1350 Ramachandran restraints generated.
    675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.7694 (pt0) cc_final: 0.7406 (pt0)
REVERT: A   88 GLN cc_start: 0.8177 (tp40) cc_final: 0.7540 (tm-30)
REVERT: A   96 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7443 (mt-10)
REVERT: A  156 ILE cc_start: 0.7203 (tp) cc_final: 0.6848 (tt)
REVERT: B   63 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6434 (pm20)
REVERT: B   99 THR cc_start: 0.8385 (t) cc_final: 0.8091 (p)
REVERT: B  147 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7598 (mt-10)
REVERT: B  194 GLU cc_start: 0.8143 (tp30) cc_final: 0.7693 (tp30)
REVERT: B  209 LYS cc_start: 0.8421 (tttp) cc_final: 0.8146 (ttpt)
REVERT: C   54 MET cc_start: 0.7666 (mmm) cc_final: 0.7195 (mmm)
REVERT: D    6 LYS cc_start: 0.5380 (ptpp) cc_final: 0.4756 (ptmt)
REVERT: E   47 GLU cc_start: 0.7754 (tp30) cc_final: 0.7299 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 132
  average time/residue: 0.5458
  time to fit residues: 75.0980
Evaluate side-chains
  136 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   96 GLU
Chi-restraints excluded: chain B residue   11 ARG
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue   29 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain D residue   30 ILE
Chi-restraints excluded: chain F residue   27 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9740

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

Flipped N/Q/H residues before XYZ refinement:
B  74 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.136847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.108107 restraints weight = 6378.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.73
r_work: 0.3091 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5384  Z= 0.125
  Angle     :  0.498   7.018   7255  Z= 0.263
  Chirality :  0.037   0.140    854
  Planarity :  0.002   0.020    908
  Dihedral  :  3.766  16.859    705
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.90 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.86 (0.33), residues: 675
  helix:  2.90 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.71 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  62 
 TYR   0.014   0.002   TYR B  17 
 PHE   0.027   0.001   PHE C  52 
 TRP   0.021   0.001   TRP G  38 
 HIS   0.009   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5384)
  covalent geometry    : angle       0.49793 ( 7255)
  hydrogen bonds       : bond        0.03476 (  405)
  hydrogen bonds       : angle       3.55056 ( 1215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2018.11 seconds
wall clock time: 35 minutes 3.85 seconds (2103.85 seconds total)