Starting phenix.real_space_refine
on Fri Sep 27 08:34:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfv_13381/09_2024/7pfv_13381.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     354      5.49       5
     S      10      5.16       5
     C    7612      2.51       5
     N    2606      2.21       5
     O    3298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 13880
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3647
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "I"
      Number of atoms: 3610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3610
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "U"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 8.09, per 1000 atoms: 0.58
  Number of scatterers: 13880
  At special positions: 0
  Unit cell: (137.55, 90.3, 139.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     354     15.00
     O    3298      8.00
     N    2606      7.00
     C    7612      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: 3.17
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 11 sheets defined
      70.0% alpha, 3.3% beta
      173 base pairs and 312 stacking pairs defined.
    Time for finding SS restraints: 6.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.769A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.704A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.950A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.279A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.534A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.643A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.621A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.125A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.279A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.508A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 38 through 49
      removed outlier: 3.951A  pdb=" N   LEU U  42 " --> pdb=" O   PRO U  38 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 58 through 69
    Processing helix  chain 'U' and resid 75 through 89
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.746A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.221A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.967A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.490A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.777A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.408A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'U' and resid 56 through 57

    437 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      445 hydrogen bonds
      890 hydrogen bond angles
      0 basepair planarities
      173 basepair parallelities
      312 stacking parallelities
  Total time for adding SS restraints: 6.38

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2439
        1.33 -     1.45: 5131
        1.45 -     1.57: 6550
        1.57 -     1.69: 706
        1.69 -     1.81: 20
  Bond restraints: 14846
  Sorted by residual:
  bond pdb=" CD  GLU A  97 "
       pdb=" OE1 GLU A  97 "
    ideal  model  delta    sigma   weight residual
    1.249  1.211  0.038 1.90e-02 2.77e+03 4.01e+00
  bond pdb=" CG  GLU A 105 "
       pdb=" CD  GLU A 105 "
    ideal  model  delta    sigma   weight residual
    1.516  1.466  0.050 2.50e-02 1.60e+03 3.94e+00
  bond pdb=" CG  GLU A  97 "
       pdb=" CD  GLU A  97 "
    ideal  model  delta    sigma   weight residual
    1.516  1.467  0.049 2.50e-02 1.60e+03 3.81e+00
  bond pdb=" C3'  DG I 158 "
       pdb=" O3'  DG I 158 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.69e+00
  bond pdb=" CD  GLU B  74 "
       pdb=" OE1 GLU B  74 "
    ideal  model  delta    sigma   weight residual
    1.249  1.214  0.035 1.90e-02 2.77e+03 3.36e+00
  ... (remaining 14841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 20887
        2.16 -     4.31: 609
        4.31 -     6.47: 44
        6.47 -     8.62: 20
        8.62 -    10.78: 3
  Bond angle restraints: 21563
  Sorted by residual:
  angle pdb=" CA  GLU A  97 "
        pdb=" CB  GLU A  97 "
        pdb=" CG  GLU A  97 "
      ideal   model   delta    sigma   weight residual
     114.10  124.88  -10.78 2.00e+00 2.50e-01 2.90e+01
  angle pdb=" N   GLU A  97 "
        pdb=" CA  GLU A  97 "
        pdb=" CB  GLU A  97 "
      ideal   model   delta    sigma   weight residual
     110.39  118.91   -8.52 1.66e+00 3.63e-01 2.63e+01
  angle pdb=" N   GLU A 105 "
        pdb=" CA  GLU A 105 "
        pdb=" CB  GLU A 105 "
      ideal   model   delta    sigma   weight residual
     110.28  117.86   -7.58 1.55e+00 4.16e-01 2.39e+01
  angle pdb=" N   GLU B  74 "
        pdb=" CA  GLU B  74 "
        pdb=" CB  GLU B  74 "
      ideal   model   delta    sigma   weight residual
     110.28  117.50   -7.22 1.55e+00 4.16e-01 2.17e+01
  angle pdb=" N   GLU A  94 "
        pdb=" CA  GLU A  94 "
        pdb=" CB  GLU A  94 "
      ideal   model   delta    sigma   weight residual
     110.22  117.34   -7.12 1.54e+00 4.22e-01 2.14e+01
  ... (remaining 21558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 6021
       35.35 -    70.70: 1934
       70.70 -   106.05: 48
      106.05 -   141.40: 2
      141.40 -   176.75: 2
  Dihedral angle restraints: 8007
    sinusoidal: 5576
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   GLN A  85 "
           pdb=" CA  GLN A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.22   24.78     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  ILE F  50 "
           pdb=" C   ILE F  50 "
           pdb=" N   TYR F  51 "
           pdb=" CA  TYR F  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.41  -22.59     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.06   20.94     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 8004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1798
       0.046 -    0.092: 526
       0.092 -    0.137: 115
       0.137 -    0.183: 14
       0.183 -    0.229: 3
  Chirality restraints: 2456
  Sorted by residual:
  chirality pdb=" CA  ARG B  23 "
            pdb=" N   ARG B  23 "
            pdb=" C   ARG B  23 "
            pdb=" CB  ARG B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  GLU H  71 "
            pdb=" N   GLU H  71 "
            pdb=" C   GLU H  71 "
            pdb=" CB  GLU H  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  GLU A  97 "
            pdb=" N   GLU A  97 "
            pdb=" C   GLU A  97 "
            pdb=" CB  GLU A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2453 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 101 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.10e+00
        pdb=" C   VAL A 101 "    0.052 2.00e-02 2.50e+03
        pdb=" O   VAL A 101 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLY A 102 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  70 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.62e+00
        pdb=" C   VAL B  70 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B  70 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B  71 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  61 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" CD  GLU C  61 "    0.049 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  61 "   -0.018 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  61 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2905
        2.78 -     3.31: 12957
        3.31 -     3.84: 30777
        3.84 -     4.37: 34193
        4.37 -     4.90: 46781
  Nonbonded interactions: 127613
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B  23 "
            pdb=" OD1 ASP B  24 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OD1 ASP A 123 "
            pdb=" NE2 HIS E 113 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OG  SER G  40 "
            pdb=" O   ARG G  42 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OP1  DT J 649 "
            pdb=" NH1 ARG U  53 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OG  SER C  40 "
            pdb=" O   ARG C  42 "
     model   vdw
     2.307 3.040
  ... (remaining 127608 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     37.640
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
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   0.058  14846  Z= 0.334
  Angle     :  0.865  10.776  21563  Z= 0.502
  Chirality :  0.045   0.229   2456
  Planarity :  0.007   0.091   1498
  Dihedral  : 30.434 176.752   6441
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  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:  0.36 (0.26), residues: 825
  helix:  0.67 (0.20), residues: 575
  sheet: -2.49 (1.47), residues: 10
  loop : -0.45 (0.34), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS B  75 
 PHE   0.020   0.002   PHE E 104 
 TYR   0.021   0.003   TYR C  39 
 ARG   0.016   0.001   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9120 (t80) cc_final: 0.8848 (t80)
REVERT: A   90 MET cc_start: 0.9710 (mmp) cc_final: 0.9504 (mmm)
REVERT: A   94 GLU cc_start: 0.9479 (mp0) cc_final: 0.8979 (pm20)
REVERT: A  120 MET cc_start: 0.8395 (mtm) cc_final: 0.7748 (mpp)
REVERT: B   53 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9011 (tm-30)
REVERT: B   63 GLU cc_start: 0.9195 (pt0) cc_final: 0.8861 (pp20)
REVERT: B   97 LEU cc_start: 0.8864 (tp) cc_final: 0.8590 (tt)
REVERT: C   61 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9103 (mt-10)
REVERT: D   82 HIS cc_start: 0.9669 (t-90) cc_final: 0.9348 (t-90)
REVERT: D  105 GLU cc_start: 0.9551 (pp20) cc_final: 0.9336 (pp20)
REVERT: D  109 HIS cc_start: 0.9850 (m-70) cc_final: 0.9645 (m90)
REVERT: F   62 LEU cc_start: 0.9856 (mt) cc_final: 0.9621 (pp)
REVERT: F   74 GLU cc_start: 0.9632 (tm-30) cc_final: 0.9366 (mt-10)
REVERT: H   62 MET cc_start: 0.9525 (mmp) cc_final: 0.9301 (tmm)
REVERT: H  105 GLU cc_start: 0.9527 (pm20) cc_final: 0.9309 (pm20)
REVERT: H  106 LEU cc_start: 0.9869 (mt) cc_final: 0.9621 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2923
  time to fit residues: 42.1576
Evaluate side-chains
  70 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  14846  Z= 0.420
  Angle     :  0.738   6.822  21563  Z= 0.439
  Chirality :  0.040   0.180   2456
  Planarity :  0.005   0.050   1498
  Dihedral  : 33.885 174.805   4789
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  3.61 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.43 (0.27), residues: 825
  helix:  1.60 (0.20), residues: 570
  sheet: -1.93 (1.74), residues: 10
  loop : -0.39 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  75 
 PHE   0.016   0.002   PHE A 104 
 TYR   0.020   0.003   TYR G  39 
 ARG   0.006   0.001   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9525 (tp40) cc_final: 0.9185 (tp-100)
REVERT: A  120 MET cc_start: 0.8560 (mtm) cc_final: 0.8059 (mtt)
REVERT: B   53 GLU cc_start: 0.9263 (tm-30) cc_final: 0.9020 (tm-30)
REVERT: D   59 MET cc_start: 0.8857 (tpt) cc_final: 0.8373 (tpt)
REVERT: D   62 MET cc_start: 0.9443 (mmp) cc_final: 0.9231 (mmp)
REVERT: D   82 HIS cc_start: 0.9674 (t-90) cc_final: 0.9369 (t-90)
REVERT: G   41 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: H   57 LYS cc_start: 0.8853 (ptmm) cc_final: 0.8531 (ptmt)
REVERT: H   59 MET cc_start: 0.7631 (tpt) cc_final: 0.6997 (tpt)
REVERT: H   62 MET cc_start: 0.9524 (mmp) cc_final: 0.9236 (mmm)
REVERT: H  106 LEU cc_start: 0.9866 (mt) cc_final: 0.9599 (mt)
REVERT: H  121 TYR cc_start: 0.9682 (t80) cc_final: 0.9473 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 88
  average time/residue: 0.2903
  time to fit residues: 36.1540
Evaluate side-chains
  61 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 111 optimal weight:    0.0370
   chunk 91 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    2.0062

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14846  Z= 0.198
  Angle     :  0.610   6.166  21563  Z= 0.369
  Chirality :  0.035   0.145   2456
  Planarity :  0.004   0.043   1498
  Dihedral  : 33.242 175.313   4789
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.03 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  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:  1.99 (0.28), residues: 825
  helix:  2.00 (0.21), residues: 582
  sheet: -2.12 (1.59), residues: 10
  loop : -0.21 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.020   0.002   PHE G  25 
 TYR   0.013   0.002   TYR B  72 
 ARG   0.011   0.000   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9662 (mmp) cc_final: 0.9445 (mmm)
REVERT: A   93 GLN cc_start: 0.9658 (tp40) cc_final: 0.9140 (tm-30)
REVERT: A   97 GLU cc_start: 0.9548 (pp20) cc_final: 0.9083 (pp20)
REVERT: A  104 PHE cc_start: 0.9203 (m-80) cc_final: 0.8756 (m-80)
REVERT: A  120 MET cc_start: 0.8270 (mtm) cc_final: 0.7709 (mpp)
REVERT: B   54 THR cc_start: 0.9847 (p) cc_final: 0.9429 (p)
REVERT: D   82 HIS cc_start: 0.9656 (t-90) cc_final: 0.9322 (t-90)
REVERT: E  120 MET cc_start: 0.9220 (tpp) cc_final: 0.8995 (tpp)
REVERT: F   74 GLU cc_start: 0.9585 (tm-30) cc_final: 0.9326 (tm-30)
REVERT: G   41 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8704 (tm-30)
REVERT: H   62 MET cc_start: 0.9575 (mmp) cc_final: 0.9349 (mmm)
REVERT: H  106 LEU cc_start: 0.9852 (mt) cc_final: 0.9496 (mt)
REVERT: H  121 TYR cc_start: 0.9639 (t80) cc_final: 0.9402 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 98
  average time/residue: 0.3050
  time to fit residues: 42.1546
Evaluate side-chains
  68 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   chunk 109 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  55 GLN
E  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  14846  Z= 0.341
  Angle     :  0.666   5.812  21563  Z= 0.399
  Chirality :  0.037   0.162   2456
  Planarity :  0.005   0.060   1498
  Dihedral  : 33.455 178.708   4789
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  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:  1.77 (0.28), residues: 825
  helix:  1.79 (0.21), residues: 582
  sheet: -1.77 (1.79), residues: 10
  loop : -0.21 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  75 
 PHE   0.015   0.002   PHE E 104 
 TYR   0.016   0.002   TYR G  39 
 ARG   0.004   0.001   ARG E  83 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9630 (mmp) cc_final: 0.9367 (mmm)
REVERT: A   93 GLN cc_start: 0.9630 (tp40) cc_final: 0.9186 (tm-30)
REVERT: A   94 GLU cc_start: 0.9399 (mp0) cc_final: 0.8930 (mp0)
REVERT: A   97 GLU cc_start: 0.9539 (pp20) cc_final: 0.9016 (pp20)
REVERT: A  104 PHE cc_start: 0.9331 (m-10) cc_final: 0.8940 (m-80)
REVERT: A  120 MET cc_start: 0.8310 (mtm) cc_final: 0.7795 (mtt)
REVERT: D   62 MET cc_start: 0.9348 (mmp) cc_final: 0.9119 (mmp)
REVERT: D   82 HIS cc_start: 0.9669 (t-90) cc_final: 0.9366 (t-90)
REVERT: D  105 GLU cc_start: 0.9511 (pp20) cc_final: 0.9266 (pp20)
REVERT: D  108 LYS cc_start: 0.9669 (mtmm) cc_final: 0.9447 (ptpp)
REVERT: E  104 PHE cc_start: 0.9569 (m-10) cc_final: 0.9361 (m-80)
REVERT: F   74 GLU cc_start: 0.9644 (tm-30) cc_final: 0.9443 (tm-30)
REVERT: H   62 MET cc_start: 0.9549 (mmp) cc_final: 0.9345 (mmp)
REVERT: H  105 GLU cc_start: 0.9504 (pm20) cc_final: 0.9296 (pm20)
REVERT: H  106 LEU cc_start: 0.9846 (mt) cc_final: 0.9620 (mt)
REVERT: H  121 TYR cc_start: 0.9611 (t80) cc_final: 0.9299 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2811
  time to fit residues: 32.9881
Evaluate side-chains
  59 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 93 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   chunk 98 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
F  27 GLN
F  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  14846  Z= 0.430
  Angle     :  0.749   7.420  21563  Z= 0.440
  Chirality :  0.040   0.164   2456
  Planarity :  0.005   0.048   1498
  Dihedral  : 34.074 179.595   4789
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 26.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.46 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.05 (0.28), residues: 825
  helix:  1.29 (0.21), residues: 576
  sheet: -1.47 (1.83), residues: 10
  loop : -0.54 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS B  75 
 PHE   0.021   0.003   PHE E 104 
 TYR   0.016   0.002   TYR H  37 
 ARG   0.006   0.001   ARG A  83 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9651 (mmp) cc_final: 0.9368 (mmm)
REVERT: A   93 GLN cc_start: 0.9658 (tp40) cc_final: 0.9193 (tm-30)
REVERT: A   97 GLU cc_start: 0.9551 (pp20) cc_final: 0.9125 (pp20)
REVERT: A  104 PHE cc_start: 0.9317 (m-10) cc_final: 0.8852 (m-80)
REVERT: A  120 MET cc_start: 0.8474 (mtm) cc_final: 0.7941 (mtt)
REVERT: B   20 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7646 (mmtt)
REVERT: D   62 MET cc_start: 0.9423 (mmp) cc_final: 0.9215 (mmp)
REVERT: D   82 HIS cc_start: 0.9665 (t-90) cc_final: 0.9431 (t-90)
REVERT: D  105 GLU cc_start: 0.9469 (pp20) cc_final: 0.9248 (pp20)
REVERT: E  106 ASP cc_start: 0.9658 (m-30) cc_final: 0.9438 (m-30)
REVERT: H   59 MET cc_start: 0.7989 (tpt) cc_final: 0.7736 (tpt)
REVERT: H  106 LEU cc_start: 0.9839 (mt) cc_final: 0.9542 (mt)
REVERT: H  121 TYR cc_start: 0.9543 (t80) cc_final: 0.9167 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.2834
  time to fit residues: 32.6867
Evaluate side-chains
  52 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 109 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
D 109 HIS
H 109 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14846  Z= 0.240
  Angle     :  0.640   5.860  21563  Z= 0.383
  Chirality :  0.036   0.146   2456
  Planarity :  0.004   0.064   1498
  Dihedral  : 33.608 173.964   4789
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.75 (0.29), residues: 825
  helix:  1.86 (0.21), residues: 570
  sheet: -1.50 (1.81), residues: 10
  loop : -0.34 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  75 
 PHE   0.013   0.002   PHE G  25 
 TYR   0.010   0.002   TYR C  39 
 ARG   0.005   0.000   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9655 (mmp) cc_final: 0.9402 (mmm)
REVERT: A   93 GLN cc_start: 0.9625 (tp40) cc_final: 0.9164 (tm-30)
REVERT: A   94 GLU cc_start: 0.9434 (mp0) cc_final: 0.8895 (mp0)
REVERT: A   97 GLU cc_start: 0.9516 (pp20) cc_final: 0.8991 (pp20)
REVERT: A  104 PHE cc_start: 0.9310 (m-10) cc_final: 0.8833 (m-80)
REVERT: A  120 MET cc_start: 0.8254 (mtm) cc_final: 0.7759 (mtt)
REVERT: B   20 LYS cc_start: 0.8019 (mmpt) cc_final: 0.7703 (mmtt)
REVERT: B   63 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9103 (pt0)
REVERT: D   62 MET cc_start: 0.9278 (mmp) cc_final: 0.8989 (mmp)
REVERT: D   82 HIS cc_start: 0.9638 (t-90) cc_final: 0.9391 (t-90)
REVERT: D  105 GLU cc_start: 0.9439 (pp20) cc_final: 0.9228 (pp20)
REVERT: D  108 LYS cc_start: 0.9658 (mtmm) cc_final: 0.9412 (ptpp)
REVERT: D  109 HIS cc_start: 0.9757 (m90) cc_final: 0.9254 (m170)
REVERT: E  106 ASP cc_start: 0.9568 (m-30) cc_final: 0.9304 (m-30)
REVERT: F   74 GLU cc_start: 0.9593 (tm-30) cc_final: 0.9371 (tm-30)
REVERT: H  105 GLU cc_start: 0.9567 (pm20) cc_final: 0.9199 (pm20)
REVERT: H  106 LEU cc_start: 0.9867 (mt) cc_final: 0.9474 (mt)
REVERT: H  109 HIS cc_start: 0.9662 (m90) cc_final: 0.9295 (m-70)
REVERT: H  121 TYR cc_start: 0.9604 (t80) cc_final: 0.9259 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2667
  time to fit residues: 36.3799
Evaluate side-chains
  64 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 92 optimal weight:    7.9990
   chunk 108 optimal weight:   30.0000
   chunk 68 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  14846  Z= 0.190
  Angle     :  0.609   6.319  21563  Z= 0.364
  Chirality :  0.035   0.149   2456
  Planarity :  0.004   0.063   1498
  Dihedral  : 33.047 177.084   4789
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.94 (0.29), residues: 825
  helix:  1.96 (0.21), residues: 578
  sheet: -1.70 (1.69), residues: 10
  loop : -0.22 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.028   0.002   PHE G  25 
 TYR   0.015   0.002   TYR E  99 
 ARG   0.004   0.000   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9624 (mmp) cc_final: 0.9362 (mmm)
REVERT: A   93 GLN cc_start: 0.9484 (tp40) cc_final: 0.9109 (tm-30)
REVERT: A   94 GLU cc_start: 0.9407 (mp0) cc_final: 0.8875 (mp0)
REVERT: A   97 GLU cc_start: 0.9491 (pp20) cc_final: 0.8961 (pp20)
REVERT: A  104 PHE cc_start: 0.9310 (m-10) cc_final: 0.8861 (m-80)
REVERT: A  120 MET cc_start: 0.7849 (mtm) cc_final: 0.7311 (mpp)
REVERT: B   20 LYS cc_start: 0.7992 (mmpt) cc_final: 0.7554 (mmtt)
REVERT: B   63 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9016 (mp0)
REVERT: D   82 HIS cc_start: 0.9608 (t-90) cc_final: 0.9342 (t-90)
REVERT: D  105 GLU cc_start: 0.9472 (pp20) cc_final: 0.9166 (pp20)
REVERT: D  108 LYS cc_start: 0.9635 (mtmm) cc_final: 0.9350 (ptpp)
REVERT: D  109 HIS cc_start: 0.9777 (m90) cc_final: 0.9166 (m170)
REVERT: E  106 ASP cc_start: 0.9527 (m-30) cc_final: 0.9266 (m-30)
REVERT: E  120 MET cc_start: 0.9251 (tpp) cc_final: 0.9040 (tpp)
REVERT: F   74 GLU cc_start: 0.9603 (tm-30) cc_final: 0.9377 (tm-30)
REVERT: H  105 GLU cc_start: 0.9588 (pm20) cc_final: 0.9238 (pm20)
REVERT: H  106 LEU cc_start: 0.9847 (mt) cc_final: 0.9522 (mt)
REVERT: H  121 TYR cc_start: 0.9584 (t80) cc_final: 0.9217 (t80)
REVERT: U   86 LEU cc_start: 0.9185 (tp) cc_final: 0.8671 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2926
  time to fit residues: 38.1684
Evaluate side-chains
  65 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  14846  Z= 0.268
  Angle     :  0.632   7.059  21563  Z= 0.378
  Chirality :  0.036   0.143   2456
  Planarity :  0.004   0.046   1498
  Dihedral  : 33.145 179.237   4789
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.94 (0.29), residues: 825
  helix:  2.04 (0.21), residues: 568
  sheet: -1.73 (1.73), residues: 10
  loop : -0.32 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.029   0.003   PHE E 104 
 TYR   0.020   0.002   TYR E  99 
 ARG   0.004   0.000   ARG E  69 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9644 (mmp) cc_final: 0.9361 (mmm)
REVERT: A   93 GLN cc_start: 0.9505 (tp40) cc_final: 0.9120 (tm-30)
REVERT: A   94 GLU cc_start: 0.9456 (mp0) cc_final: 0.8990 (mp0)
REVERT: A   97 GLU cc_start: 0.9509 (pp20) cc_final: 0.8963 (pp20)
REVERT: A  104 PHE cc_start: 0.9270 (m-10) cc_final: 0.8776 (m-80)
REVERT: B   20 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7612 (mmtt)
REVERT: B   63 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9115 (pt0)
REVERT: D   82 HIS cc_start: 0.9616 (t-90) cc_final: 0.9365 (t-90)
REVERT: D  108 LYS cc_start: 0.9660 (mtmm) cc_final: 0.9390 (ptpp)
REVERT: D  109 HIS cc_start: 0.9744 (m90) cc_final: 0.9354 (m170)
REVERT: E  120 MET cc_start: 0.9275 (tpp) cc_final: 0.9071 (tpp)
REVERT: H   62 MET cc_start: 0.9476 (mmp) cc_final: 0.9275 (mmp)
REVERT: H  106 LEU cc_start: 0.9850 (mt) cc_final: 0.9538 (mt)
REVERT: H  121 TYR cc_start: 0.9559 (t80) cc_final: 0.9164 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.3034
  time to fit residues: 37.7415
Evaluate side-chains
  61 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   overall best weight:    2.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14846  Z= 0.237
  Angle     :  0.627   6.325  21563  Z= 0.375
  Chirality :  0.035   0.142   2456
  Planarity :  0.004   0.062   1498
  Dihedral  : 33.061 178.936   4789
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  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:  1.87 (0.29), residues: 825
  helix:  1.91 (0.21), residues: 580
  sheet: -1.78 (1.70), residues: 10
  loop : -0.26 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.021   0.002   PHE G  25 
 TYR   0.018   0.002   TYR E  99 
 ARG   0.013   0.000   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9663 (mmp) cc_final: 0.9450 (mmm)
REVERT: A   93 GLN cc_start: 0.9497 (tp40) cc_final: 0.9122 (tp-100)
REVERT: A   94 GLU cc_start: 0.9433 (mp0) cc_final: 0.9070 (mp0)
REVERT: A   97 GLU cc_start: 0.9493 (pp20) cc_final: 0.9042 (pp20)
REVERT: A  104 PHE cc_start: 0.9297 (m-10) cc_final: 0.8836 (m-80)
REVERT: B   20 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7732 (mmtt)
REVERT: C   41 GLU cc_start: 0.9390 (pm20) cc_final: 0.8920 (pp20)
REVERT: D   82 HIS cc_start: 0.9608 (t-90) cc_final: 0.9354 (t-90)
REVERT: D  108 LYS cc_start: 0.9648 (mtmm) cc_final: 0.9377 (ptpp)
REVERT: D  109 HIS cc_start: 0.9742 (m90) cc_final: 0.9351 (m170)
REVERT: E  120 MET cc_start: 0.9266 (tpp) cc_final: 0.9060 (tpp)
REVERT: F   74 GLU cc_start: 0.9590 (tm-30) cc_final: 0.9373 (tm-30)
REVERT: H  121 TYR cc_start: 0.9554 (t80) cc_final: 0.9154 (t80)
REVERT: U   86 LEU cc_start: 0.9162 (tp) cc_final: 0.8640 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.3011
  time to fit residues: 39.4035
Evaluate side-chains
  66 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 89 optimal weight:   30.0000
   chunk 9 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14846  Z= 0.277
  Angle     :  0.649   6.936  21563  Z= 0.388
  Chirality :  0.036   0.177   2456
  Planarity :  0.004   0.054   1498
  Dihedral  : 33.143 179.683   4789
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  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:  1.69 (0.29), residues: 825
  helix:  1.75 (0.21), residues: 588
  sheet: -1.69 (1.75), residues: 10
  loop : -0.34 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS B  75 
 PHE   0.021   0.002   PHE E 104 
 TYR   0.019   0.002   TYR E  99 
 ARG   0.010   0.000   ARG B  23 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9513 (tp40) cc_final: 0.9137 (tp-100)
REVERT: A   94 GLU cc_start: 0.9433 (mp0) cc_final: 0.9048 (mp0)
REVERT: A   97 GLU cc_start: 0.9495 (pp20) cc_final: 0.9050 (pp20)
REVERT: A  104 PHE cc_start: 0.9285 (m-10) cc_final: 0.8783 (m-80)
REVERT: B   20 LYS cc_start: 0.7907 (mmpt) cc_final: 0.7604 (mmtt)
REVERT: B   63 GLU cc_start: 0.9264 (mp0) cc_final: 0.9045 (mp0)
REVERT: C   41 GLU cc_start: 0.9372 (pm20) cc_final: 0.8914 (pp20)
REVERT: D   82 HIS cc_start: 0.9620 (t-90) cc_final: 0.9379 (t-90)
REVERT: D  108 LYS cc_start: 0.9654 (mtmm) cc_final: 0.9387 (ptpp)
REVERT: D  109 HIS cc_start: 0.9738 (m90) cc_final: 0.9355 (m170)
REVERT: E  120 MET cc_start: 0.9273 (tpp) cc_final: 0.9068 (tpp)
REVERT: H  105 GLU cc_start: 0.9566 (pm20) cc_final: 0.9158 (pm20)
REVERT: H  106 LEU cc_start: 0.9839 (mt) cc_final: 0.9377 (mt)
REVERT: H  109 HIS cc_start: 0.9514 (m90) cc_final: 0.9138 (m-70)
REVERT: H  121 TYR cc_start: 0.9541 (t80) cc_final: 0.9132 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2579
  time to fit residues: 32.6179
Evaluate side-chains
  62 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 89 optimal weight:   30.0000
   chunk 37 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 16 optimal weight:    0.3980
   chunk 78 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   overall best weight:    3.6586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.027304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.020866 restraints weight = 232372.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.021536 restraints weight = 110982.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.021992 restraints weight = 66785.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  14846  Z= 0.270
  Angle     :  0.651   6.453  21563  Z= 0.388
  Chirality :  0.036   0.149   2456
  Planarity :  0.004   0.048   1498
  Dihedral  : 33.178 179.575   4789
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  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:  1.63 (0.29), residues: 825
  helix:  1.70 (0.21), residues: 588
  sheet: -1.37 (1.79), residues: 10
  loop : -0.36 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.021   0.002   PHE G  25 
 TYR   0.015   0.002   TYR E  99 
 ARG   0.009   0.000   ARG B  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1919.02 seconds
wall clock time: 35 minutes 48.12 seconds (2148.12 seconds total)