Starting phenix.real_space_refine
on Thu Feb 15 09:12:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfn_33177/02_2024/7xfn_33177_updated.pdb"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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: 5
    Type Number    sf(0)   Gaussians
     P     285      5.49       5
     S      12      5.16       5
     C    6540      2.51       5
     N    2225      2.21       5
     O    2769      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  133": "OE1" <-> "OE2"
    Residue "F TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 11831
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 825
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2948
          Classifications: {'DNA': 143}
          Link IDs: {'rna3p': 142}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "J"
      Number of atoms: 2911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 2911
          Classifications: {'DNA': 143}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 142}
  Time building chain proxies: 6.68, per 1000 atoms: 0.56
  Number of scatterers: 11831
  At special positions: 0
  Unit cell: (116.772, 123.084, 110.46, 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      12     16.00
     P     285     15.00
     O    2769      8.00
     N    2225      7.00
     C    6540      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  - 3.50
        Amino acid           : False - 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: 6.00
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      64.0% alpha, 0.0% beta
      136 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 7.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 56
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 4.020A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 113
    Processing helix  chain 'A' and resid 121 through 131
    Processing helix  chain 'B' and resid 26 through 28
      No H-bonds generated for 'chain 'B' and resid 26 through 28'
    Processing helix  chain 'B' and resid 31 through 40
    Processing helix  chain 'B' and resid 50 through 75
      removed outlier: 3.737A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 27 through 35
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 4.282A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 88
    Processing helix  chain 'C' and resid 91 through 96
    Processing helix  chain 'D' and resid 35 through 45
    Processing helix  chain 'D' and resid 53 through 80
    Processing helix  chain 'D' and resid 88 through 98
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 45 through 54
    Processing helix  chain 'E' and resid 64 through 77
      removed outlier: 4.283A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 113
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'F' and resid 26 through 28
      No H-bonds generated for 'chain 'F' and resid 26 through 28'
    Processing helix  chain 'F' and resid 31 through 40
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.566A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 92
    Processing helix  chain 'G' and resid 17 through 20
      No H-bonds generated for 'chain 'G' and resid 17 through 20'
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.310A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 89
    Processing helix  chain 'G' and resid 91 through 96
    Processing helix  chain 'H' and resid 35 through 45
      removed outlier: 3.531A  pdb=" N   TYR H  39 " --> pdb=" O   ALA H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 53 through 80
    Processing helix  chain 'H' and resid 88 through 98
    Processing helix  chain 'H' and resid 101 through 120

    340 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
Warning, Cannot make NA restraints for ID residue
Warning, Cannot make NA restraints for ID residue
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 4.23

  Time building geometry restraints manager: 6.32 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: 2103
        1.33 -     1.45: 4228
        1.45 -     1.57: 5701
        1.57 -     1.69: 569
        1.69 -     1.81: 22
  Bond restraints: 12623
  Sorted by residual:
  bond pdb=" C4'  DI I -55 "
       pdb=" O4'  DI I -55 "
    ideal  model  delta    sigma   weight residual
    1.640  1.432  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C3'  DI I -55 "
       pdb=" C4'  DI I -55 "
    ideal  model  delta    sigma   weight residual
    1.315  1.519 -0.204 2.00e-02 2.50e+03 1.04e+02
  bond pdb=" C4   DI I -55 "
       pdb=" N3   DI I -55 "
    ideal  model  delta    sigma   weight residual
    1.507  1.353  0.154 2.00e-02 2.50e+03 5.93e+01
  bond pdb=" C2   DI I -55 "
       pdb=" N3   DI I -55 "
    ideal  model  delta    sigma   weight residual
    1.482  1.343  0.139 2.00e-02 2.50e+03 4.81e+01
  bond pdb=" C1'  DI I -55 "
       pdb=" O4'  DI I -55 "
    ideal  model  delta    sigma   weight residual
    1.311  1.429 -0.118 2.00e-02 2.50e+03 3.46e+01
  ... (remaining 12618 not shown)

  Histogram of bond angle deviations from ideal:
       97.92 -   105.60: 1454
      105.60 -   113.28: 7096
      113.28 -   120.95: 6081
      120.95 -   128.63: 3417
      128.63 -   136.31: 226
  Bond angle restraints: 18274
  Sorted by residual:
  angle pdb=" C1'  DI I -55 "
        pdb=" N9   DI I -55 "
        pdb=" C4   DI I -55 "
      ideal   model   delta    sigma   weight residual
     107.36  125.01  -17.65 3.00e+00 1.11e-01 3.46e+01
  angle pdb=" N   GLU H 110 "
        pdb=" CA  GLU H 110 "
        pdb=" CB  GLU H 110 "
      ideal   model   delta    sigma   weight residual
     110.28  118.08   -7.80 1.55e+00 4.16e-01 2.53e+01
  angle pdb=" C1'  DI I -55 "
        pdb=" N9   DI I -55 "
        pdb=" C8   DI I -55 "
      ideal   model   delta    sigma   weight residual
     138.51  126.42   12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C3'  DC J  21 "
        pdb=" O3'  DC J  21 "
        pdb=" P    DC J  22 "
      ideal   model   delta    sigma   weight residual
     120.20  125.86   -5.66 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" CG  ARG B  92 "
        pdb=" CD  ARG B  92 "
        pdb=" NE  ARG B  92 "
      ideal   model   delta    sigma   weight residual
     112.00  103.98    8.02 2.20e+00 2.07e-01 1.33e+01
  ... (remaining 18269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 5471
       35.36 -    70.71: 1358
       70.71 -   106.07: 15
      106.07 -   141.42: 3
      141.42 -   176.78: 2
  Dihedral angle restraints: 6849
    sinusoidal: 4668
      harmonic: 2181
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.78 -176.78     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J  21 "
           pdb=" C3'  DC J  21 "
           pdb=" O3'  DC J  21 "
           pdb=" P    DC J  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.90  165.10     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 6846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1755
       0.057 -    0.115: 285
       0.115 -    0.172: 34
       0.172 -    0.230: 4
       0.230 -    0.287: 1
  Chirality restraints: 2079
  Sorted by residual:
  chirality pdb=" C3'  DI I -55 "
            pdb=" C2'  DI I -55 "
            pdb=" C4'  DI I -55 "
            pdb=" O3'  DI I -55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.70    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CB  VAL D  45 "
            pdb=" CA  VAL D  45 "
            pdb=" CG1 VAL D  45 "
            pdb=" CG2 VAL D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  GLU H 110 "
            pdb=" N   GLU H 110 "
            pdb=" C   GLU H 110 "
            pdb=" CB  GLU H 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 2076 not shown)

  Planarity restraints: 1324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  50 "   -0.024 2.00e-02 2.50e+03   2.20e-02 9.67e+00
        pdb=" CG  TYR C  50 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  50 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  50 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  50 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  50 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  50 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "   -0.045 5.00e-02 4.00e+02   6.80e-02 7.40e+00
        pdb=" N   PRO C  80 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.043 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO G  80 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1321 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2504
        2.81 -     3.33: 9456
        3.33 -     3.85: 23837
        3.85 -     4.38: 27959
        4.38 -     4.90: 39118
  Nonbonded interactions: 102874
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  87 "
            pdb=" OE1 GLU D  90 "
     model   vdw
     2.282 2.440
  nonbonded pdb=" O   THR G  16 "
            pdb=" OG  SER G  19 "
     model   vdw
     2.359 2.440
  nonbonded pdb=" OG1 THR E 118 "
            pdb=" OP1  DG J  -3 "
     model   vdw
     2.362 2.440
  nonbonded pdb=" N2   DG I -21 "
            pdb=" O2   DC J  21 "
     model   vdw
     2.372 2.496
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.388 2.440
  ... (remaining 102869 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 133)
  selection = (chain 'E' and resid 39 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 117)
}
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 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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.330
  Check model and map are aligned:         0.180
  Set scattering table:                    0.100
  Process input model:                     40.860
  Find NCS groups from input model:        0.480
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
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   0.208  12623  Z= 0.312
  Angle     :  0.768  17.646  18274  Z= 0.438
  Chirality :  0.043   0.287   2079
  Planarity :  0.007   0.085   1324
  Dihedral  : 27.815 176.780   5443
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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: -0.88 (0.26), residues: 737
  helix: -0.39 (0.19), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.67 (0.38), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.035   0.003   PHE C  25 
 TYR   0.051   0.002   TYR C  50 
 ARG   0.017   0.001   ARG H  96 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   58 THR cc_start: 0.8338 (p) cc_final: 0.8120 (p)
REVERT: A   73 GLU cc_start: 0.7990 (tt0) cc_final: 0.7670 (tt0)
REVERT: C   99 ARG cc_start: 0.7221 (mmm160) cc_final: 0.6882 (mmp-170)
REVERT: C  104 GLN cc_start: 0.7519 (mm110) cc_final: 0.7044 (mt0)
REVERT: D  113 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7560 (tttm)
REVERT: D  117 LYS cc_start: 0.7960 (tttp) cc_final: 0.7558 (tttt)
REVERT: E   63 ARG cc_start: 0.8343 (mmp80) cc_final: 0.8113 (mmt-90)
REVERT: E   97 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: F   52 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6842 (tp30)
REVERT: F   59 LYS cc_start: 0.7799 (tttp) cc_final: 0.7502 (tppt)
REVERT: G   42 ARG cc_start: 0.7365 (mtp85) cc_final: 0.7034 (mtp85)
REVERT: G   71 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7243 (ttp80)
REVERT: G   95 LYS cc_start: 0.7372 (ttmt) cc_final: 0.7125 (ttmt)
REVERT: G  101 THR cc_start: 0.8440 (m) cc_final: 0.8063 (m)
REVERT: H   40 LYS cc_start: 0.7655 (mttt) cc_final: 0.7345 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 2.0987
  time to fit residues: 360.1803
Evaluate side-chains
  106 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  27 GLN
B  93 GLN
C  24 GLN
D  60 ASN
G  31 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  12623  Z= 0.346
  Angle     :  0.682   8.903  18274  Z= 0.395
  Chirality :  0.040   0.159   2079
  Planarity :  0.006   0.052   1324
  Dihedral  : 31.292 179.353   3959
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.64 %
    Favored  : 85.12 %
  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:  0.62 (0.28), residues: 737
  helix:  0.87 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.64 (0.36), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS H 106 
 PHE   0.036   0.004   PHE G  25 
 TYR   0.018   0.003   TYR G  57 
 ARG   0.010   0.001   ARG A 131 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8002 (mttt) cc_final: 0.7510 (mmtt)
REVERT: A   73 GLU cc_start: 0.8317 (tt0) cc_final: 0.8004 (tt0)
REVERT: A  122 LYS cc_start: 0.8137 (pttt) cc_final: 0.7863 (pttp)
REVERT: B   59 LYS cc_start: 0.8169 (tttp) cc_final: 0.7967 (tttp)
REVERT: B   63 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: C   55 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8101 (mt)
REVERT: C   99 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6909 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6899 (mm-40) cc_final: 0.5746 (mm110)
REVERT: D   43 LYS cc_start: 0.8022 (mptt) cc_final: 0.7024 (mppt)
REVERT: D   68 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6772 (mm-30)
REVERT: D   73 GLU cc_start: 0.7867 (tp30) cc_final: 0.7553 (tp30)
REVERT: D  113 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7510 (tttt)
REVERT: D  117 LYS cc_start: 0.7956 (tttp) cc_final: 0.7481 (tttt)
REVERT: F   52 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7061 (tp30)
REVERT: F   59 LYS cc_start: 0.7880 (tttp) cc_final: 0.7639 (tppt)
REVERT: F   77 LYS cc_start: 0.7671 (mtmm) cc_final: 0.7328 (mttm)
REVERT: G  101 THR cc_start: 0.8370 (m) cc_final: 0.8085 (m)
REVERT: H   40 LYS cc_start: 0.7831 (mttt) cc_final: 0.7543 (mttm)
REVERT: H   57 SER cc_start: 0.8293 (t) cc_final: 0.7945 (m)
REVERT: H   68 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6959 (mp0)
REVERT: H  105 LYS cc_start: 0.7221 (mttm) cc_final: 0.6987 (mtmm)
REVERT: H  117 LYS cc_start: 0.8258 (tttp) cc_final: 0.7997 (tttm)
  outliers start: 14
  outliers final: 5
  residues processed: 142
  average time/residue: 1.9016
  time to fit residues: 284.1373
Evaluate side-chains
  125 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain H residue   68 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
C 104 GLN
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12623  Z= 0.196
  Angle     :  0.589   6.788  18274  Z= 0.355
  Chirality :  0.035   0.126   2079
  Planarity :  0.005   0.045   1324
  Dihedral  : 31.231 178.814   3959
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.20 %
    Favored  : 81.44 %
  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:  1.39 (0.29), residues: 737
  helix:  1.50 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.60 (0.36), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 106 
 PHE   0.019   0.002   PHE D  67 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.010   0.001   ARG A 129 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.7995 (mttt) cc_final: 0.7445 (mmtt)
REVERT: A   73 GLU cc_start: 0.8288 (tt0) cc_final: 0.7961 (tt0)
REVERT: A  122 LYS cc_start: 0.8118 (pttt) cc_final: 0.7835 (pttp)
REVERT: B   59 LYS cc_start: 0.8147 (tttp) cc_final: 0.7931 (tttp)
REVERT: B   63 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: C   99 ARG cc_start: 0.7457 (mmm160) cc_final: 0.6970 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6848 (mm-40) cc_final: 0.5672 (mm110)
REVERT: D   43 LYS cc_start: 0.8065 (mptt) cc_final: 0.7077 (mppt)
REVERT: D   68 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6697 (mm-30)
REVERT: D   73 GLU cc_start: 0.7783 (tp30) cc_final: 0.7525 (tp30)
REVERT: D  113 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7531 (ttmm)
REVERT: D  117 LYS cc_start: 0.7857 (tttp) cc_final: 0.7568 (tttt)
REVERT: F   52 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7074 (tp30)
REVERT: F   59 LYS cc_start: 0.7858 (tttp) cc_final: 0.7591 (tppt)
REVERT: F   77 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7275 (mttm)
REVERT: G   92 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7189 (mt-10)
REVERT: G  101 THR cc_start: 0.8355 (m) cc_final: 0.8041 (m)
REVERT: H   40 LYS cc_start: 0.7780 (mttt) cc_final: 0.7488 (mttm)
REVERT: H   43 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8010 (mptt)
REVERT: H   57 SER cc_start: 0.8193 (t) cc_final: 0.7919 (m)
REVERT: H   68 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6905 (mp0)
REVERT: H  105 LYS cc_start: 0.7109 (mttm) cc_final: 0.6883 (mtmm)
REVERT: H  117 LYS cc_start: 0.8282 (tttp) cc_final: 0.8067 (tttm)
  outliers start: 21
  outliers final: 13
  residues processed: 133
  average time/residue: 1.9093
  time to fit residues: 267.3731
Evaluate side-chains
  135 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 26 optimal weight:    0.4980
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0020
   overall best weight:    1.2592

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12623  Z= 0.221
  Angle     :  0.582   5.783  18274  Z= 0.349
  Chirality :  0.035   0.128   2079
  Planarity :  0.005   0.045   1324
  Dihedral  : 31.123 178.858   3959
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.00 %
    Favored  : 81.12 %
  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 (0.29), residues: 737
  helix:  1.82 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.58 (0.36), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 106 
 PHE   0.013   0.002   PHE D  67 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.005   0.000   ARG A  42 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8311 (tt0) cc_final: 0.7988 (tt0)
REVERT: A  122 LYS cc_start: 0.8109 (pttt) cc_final: 0.7778 (pttp)
REVERT: A  133 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6662 (mt-10)
REVERT: B   63 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7389 (mt-10)
REVERT: C   55 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8081 (mt)
REVERT: C   99 ARG cc_start: 0.7346 (mmm160) cc_final: 0.6896 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6780 (mm-40) cc_final: 0.5746 (mm110)
REVERT: D   43 LYS cc_start: 0.8074 (mptt) cc_final: 0.7082 (mppt)
REVERT: D   68 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6714 (mm-30)
REVERT: D   73 GLU cc_start: 0.7815 (tp30) cc_final: 0.7557 (tp30)
REVERT: D  113 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7511 (ttpt)
REVERT: D  117 LYS cc_start: 0.7821 (tttp) cc_final: 0.7526 (tttt)
REVERT: F   52 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7098 (tp30)
REVERT: F   59 LYS cc_start: 0.7923 (tttp) cc_final: 0.7636 (tppt)
REVERT: F   77 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7273 (mttm)
REVERT: F   79 LYS cc_start: 0.8148 (mttm) cc_final: 0.7408 (mtmt)
REVERT: G   24 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (mp10)
REVERT: G   92 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: G  101 THR cc_start: 0.8338 (m) cc_final: 0.8010 (m)
REVERT: H   40 LYS cc_start: 0.7783 (mttt) cc_final: 0.7484 (mttm)
REVERT: H   43 LYS cc_start: 0.8260 (mmtt) cc_final: 0.8037 (mptt)
REVERT: H   44 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7127 (pt0)
REVERT: H   57 SER cc_start: 0.8179 (t) cc_final: 0.7945 (m)
REVERT: H   68 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6833 (mp0)
REVERT: H  105 LYS cc_start: 0.7124 (mttm) cc_final: 0.6900 (mtmm)
  outliers start: 18
  outliers final: 7
  residues processed: 126
  average time/residue: 2.0328
  time to fit residues: 269.3730
Evaluate side-chains
  129 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12623  Z= 0.216
  Angle     :  0.568   5.564  18274  Z= 0.341
  Chirality :  0.034   0.126   2079
  Planarity :  0.004   0.042   1324
  Dihedral  : 30.981 179.576   3959
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.48 %
    Favored  : 80.64 %
  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:  2.06 (0.29), residues: 737
  helix:  2.03 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.53 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 106 
 PHE   0.013   0.002   PHE D  67 
 TYR   0.011   0.002   TYR F  51 
 ARG   0.006   0.001   ARG A  42 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8310 (tt0) cc_final: 0.7987 (tt0)
REVERT: A  122 LYS cc_start: 0.8081 (pttt) cc_final: 0.7781 (pttp)
REVERT: A  129 ARG cc_start: 0.7137 (tpt90) cc_final: 0.6903 (tpt90)
REVERT: A  133 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6540 (mt-10)
REVERT: B   63 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7371 (mt-10)
REVERT: C   55 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (mt)
REVERT: C   99 ARG cc_start: 0.7331 (mmm160) cc_final: 0.6906 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6825 (mm-40) cc_final: 0.5798 (mm110)
REVERT: D   43 LYS cc_start: 0.8082 (mptt) cc_final: 0.7067 (mppt)
REVERT: D   68 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6653 (mm-30)
REVERT: D   73 GLU cc_start: 0.7842 (tp30) cc_final: 0.7578 (tp30)
REVERT: D  113 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7494 (ttpt)
REVERT: D  117 LYS cc_start: 0.7812 (tttp) cc_final: 0.7426 (tttt)
REVERT: E   76 GLN cc_start: 0.6917 (mt0) cc_final: 0.6683 (mt0)
REVERT: F   52 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7074 (tp30)
REVERT: F   59 LYS cc_start: 0.7932 (tttp) cc_final: 0.7666 (tppt)
REVERT: F   77 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7286 (mttm)
REVERT: F   79 LYS cc_start: 0.8168 (mttm) cc_final: 0.7420 (mtmt)
REVERT: G   24 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7542 (mp10)
REVERT: G   92 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7264 (mt-10)
REVERT: G  101 THR cc_start: 0.8313 (m) cc_final: 0.7971 (m)
REVERT: H   40 LYS cc_start: 0.7813 (mttt) cc_final: 0.7531 (mttm)
REVERT: H   44 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7142 (pt0)
REVERT: H   57 SER cc_start: 0.8230 (t) cc_final: 0.8025 (m)
REVERT: H   68 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6923 (mp0)
REVERT: H  105 LYS cc_start: 0.7183 (mttm) cc_final: 0.6936 (mtmm)
  outliers start: 18
  outliers final: 8
  residues processed: 127
  average time/residue: 1.8369
  time to fit residues: 245.8649
Evaluate side-chains
  132 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12623  Z= 0.176
  Angle     :  0.558   5.587  18274  Z= 0.338
  Chirality :  0.033   0.129   2079
  Planarity :  0.004   0.042   1324
  Dihedral  : 30.974 179.693   3959
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.28 %
    Favored  : 79.84 %
  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:  2.18 (0.30), residues: 737
  helix:  2.13 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.51 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.002   PHE D  67 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.010   0.001   ARG A  42 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8250 (tt0) cc_final: 0.7938 (tt0)
REVERT: A  122 LYS cc_start: 0.8060 (pttt) cc_final: 0.7766 (pttp)
REVERT: A  129 ARG cc_start: 0.7250 (tpt90) cc_final: 0.6934 (tpt90)
REVERT: A  133 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6540 (mt-10)
REVERT: B   63 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: C   55 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (mt)
REVERT: C   95 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7342 (ttpp)
REVERT: C   99 ARG cc_start: 0.7358 (mmm160) cc_final: 0.6910 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6828 (mm-40) cc_final: 0.5812 (mm110)
REVERT: D   43 LYS cc_start: 0.8075 (mptt) cc_final: 0.7061 (mppt)
REVERT: D   68 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6652 (mm-30)
REVERT: D   73 GLU cc_start: 0.7833 (tp30) cc_final: 0.7584 (tp30)
REVERT: D  113 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7506 (ttpt)
REVERT: D  117 LYS cc_start: 0.7812 (tttp) cc_final: 0.7515 (tttt)
REVERT: F   52 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7070 (tp30)
REVERT: F   59 LYS cc_start: 0.7933 (tttp) cc_final: 0.7669 (tppt)
REVERT: F   77 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7286 (mttm)
REVERT: F   79 LYS cc_start: 0.8158 (mttm) cc_final: 0.7410 (mtmt)
REVERT: G   24 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7536 (mp10)
REVERT: G   92 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: G  101 THR cc_start: 0.8311 (m) cc_final: 0.7949 (m)
REVERT: H   40 LYS cc_start: 0.7751 (mttt) cc_final: 0.7469 (mttm)
REVERT: H   44 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7138 (pt0)
REVERT: H   68 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: H  105 LYS cc_start: 0.7178 (mttm) cc_final: 0.6936 (mtmm)
  outliers start: 18
  outliers final: 8
  residues processed: 121
  average time/residue: 1.8902
  time to fit residues: 241.0407
Evaluate side-chains
  129 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12623  Z= 0.189
  Angle     :  0.556   5.589  18274  Z= 0.336
  Chirality :  0.034   0.127   2079
  Planarity :  0.004   0.042   1324
  Dihedral  : 30.971 179.429   3959
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.92 %
    Favored  : 79.36 %
  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:  2.22 (0.30), residues: 737
  helix:  2.17 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.54 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.002   PHE D  67 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.006   0.000   ARG A  42 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8251 (tt0) cc_final: 0.7943 (tt0)
REVERT: A  122 LYS cc_start: 0.8064 (pttt) cc_final: 0.7773 (pttp)
REVERT: A  129 ARG cc_start: 0.7110 (tpt90) cc_final: 0.6790 (tpt90)
REVERT: A  133 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6543 (mt-10)
REVERT: B   63 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7373 (mt-10)
REVERT: C   55 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8114 (mt)
REVERT: C   95 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7348 (ttpp)
REVERT: C   99 ARG cc_start: 0.7356 (mmm160) cc_final: 0.6911 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6829 (mm-40) cc_final: 0.5814 (mm110)
REVERT: D   43 LYS cc_start: 0.8075 (mptt) cc_final: 0.7059 (mppt)
REVERT: D   68 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6656 (mm-30)
REVERT: D   73 GLU cc_start: 0.7835 (tp30) cc_final: 0.7587 (tp30)
REVERT: D  113 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7507 (ttpt)
REVERT: D  117 LYS cc_start: 0.7813 (tttp) cc_final: 0.7514 (tttt)
REVERT: F   52 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7071 (tp30)
REVERT: F   59 LYS cc_start: 0.7933 (tttp) cc_final: 0.7670 (tppt)
REVERT: F   77 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7291 (mttm)
REVERT: F   79 LYS cc_start: 0.8161 (mttm) cc_final: 0.7410 (mtmt)
REVERT: G   24 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7541 (mp10)
REVERT: G   92 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7267 (mt-10)
REVERT: G  101 THR cc_start: 0.8309 (m) cc_final: 0.7948 (m)
REVERT: H   40 LYS cc_start: 0.7749 (mttt) cc_final: 0.7465 (mttm)
REVERT: H   44 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7145 (pt0)
REVERT: H   68 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6917 (mp0)
REVERT: H  105 LYS cc_start: 0.7177 (mttm) cc_final: 0.6934 (mtmm)
  outliers start: 17
  outliers final: 7
  residues processed: 120
  average time/residue: 1.8970
  time to fit residues: 239.8169
Evaluate side-chains
  127 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0040
   chunk 8 optimal weight:    0.0770
   chunk 75 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.8156

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  12623  Z= 0.340
  Angle     :  0.657   6.794  18274  Z= 0.385
  Chirality :  0.040   0.146   2079
  Planarity :  0.006   0.051   1324
  Dihedral  : 31.233 179.779   3959
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.44 %
    Favored  : 79.52 %
  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:  1.58 (0.29), residues: 737
  helix:  1.72 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.82 (0.36), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H 106 
 PHE   0.015   0.002   PHE C  25 
 TYR   0.015   0.003   TYR H  34 
 ARG   0.008   0.001   ARG B  40 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8272 (tt0) cc_final: 0.7978 (tt0)
REVERT: A  122 LYS cc_start: 0.8112 (pttt) cc_final: 0.7821 (pttp)
REVERT: A  133 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6512 (mt-10)
REVERT: B   63 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7394 (mt-10)
REVERT: C   36 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7741 (mptp)
REVERT: C   55 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8034 (mt)
REVERT: C   95 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7410 (ttpp)
REVERT: C   99 ARG cc_start: 0.7363 (mmm160) cc_final: 0.6926 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6722 (mm-40) cc_final: 0.5767 (mm110)
REVERT: D   43 LYS cc_start: 0.8108 (mptt) cc_final: 0.7076 (mppt)
REVERT: D   68 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6668 (mm-30)
REVERT: D   73 GLU cc_start: 0.7694 (tp30) cc_final: 0.7479 (tp30)
REVERT: D  113 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7560 (ttmm)
REVERT: D  117 LYS cc_start: 0.7864 (tttp) cc_final: 0.7481 (tttt)
REVERT: F   52 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7092 (tp30)
REVERT: F   59 LYS cc_start: 0.7863 (tttp) cc_final: 0.7556 (tppt)
REVERT: F   77 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7305 (mttm)
REVERT: F   79 LYS cc_start: 0.8168 (mttm) cc_final: 0.7400 (mtmt)
REVERT: G   77 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7314 (mtp180)
REVERT: G   92 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7259 (mt-10)
REVERT: G  101 THR cc_start: 0.8384 (m) cc_final: 0.8072 (m)
REVERT: H   40 LYS cc_start: 0.7905 (mttt) cc_final: 0.7622 (mttm)
REVERT: H   68 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6895 (mp0)
REVERT: H  116 THR cc_start: 0.8054 (m) cc_final: 0.7848 (t)
  outliers start: 19
  outliers final: 10
  residues processed: 129
  average time/residue: 2.0256
  time to fit residues: 274.5244
Evaluate side-chains
  137 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12623  Z= 0.302
  Angle     :  0.642   6.543  18274  Z= 0.378
  Chirality :  0.038   0.140   2079
  Planarity :  0.005   0.041   1324
  Dihedral  : 31.241 179.890   3959
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.04 %
    Favored  : 78.08 %
  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:  1.53 (0.30), residues: 737
  helix:  1.68 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.85 (0.36), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H 106 
 PHE   0.013   0.002   PHE C  25 
 TYR   0.014   0.002   TYR C  57 
 ARG   0.006   0.001   ARG A 131 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8263 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  122 LYS cc_start: 0.8110 (pttt) cc_final: 0.7820 (pttp)
REVERT: A  133 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6541 (mt-10)
REVERT: B   63 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7432 (mt-10)
REVERT: C   36 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7714 (mptp)
REVERT: C   55 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8037 (mt)
REVERT: C   95 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7404 (ttpp)
REVERT: C   99 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6882 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6715 (mm-40) cc_final: 0.5780 (mm110)
REVERT: D   43 LYS cc_start: 0.8097 (mptt) cc_final: 0.7081 (mppt)
REVERT: D   68 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6670 (mm-30)
REVERT: D  113 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7491 (tttp)
REVERT: D  117 LYS cc_start: 0.7874 (tttp) cc_final: 0.7499 (tttt)
REVERT: F   52 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7081 (tp30)
REVERT: F   59 LYS cc_start: 0.7867 (tttp) cc_final: 0.7568 (tppt)
REVERT: F   77 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7303 (mttm)
REVERT: F   79 LYS cc_start: 0.8164 (mttm) cc_final: 0.7398 (mtmt)
REVERT: G   77 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7280 (mtp180)
REVERT: G   92 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7268 (mt-10)
REVERT: G  101 THR cc_start: 0.8388 (m) cc_final: 0.8073 (m)
REVERT: H   40 LYS cc_start: 0.7860 (mttt) cc_final: 0.7572 (mttm)
REVERT: H   68 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6929 (mp0)
REVERT: H  116 THR cc_start: 0.8047 (m) cc_final: 0.7836 (t)
  outliers start: 18
  outliers final: 10
  residues processed: 130
  average time/residue: 1.9846
  time to fit residues: 271.1914
Evaluate side-chains
  135 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.0070
   chunk 66 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 48 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12623  Z= 0.197
  Angle     :  0.607   6.349  18274  Z= 0.363
  Chirality :  0.035   0.128   2079
  Planarity :  0.005   0.037   1324
  Dihedral  : 31.226 179.828   3959
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.84 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.30), residues: 737
  helix:  1.86 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.80 (0.36), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.002   PHE D  67 
 TYR   0.013   0.002   TYR H  34 
 ARG   0.008   0.001   ARG A  42 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8264 (tt0) cc_final: 0.7971 (tt0)
REVERT: A  122 LYS cc_start: 0.8084 (pttt) cc_final: 0.7796 (pttp)
REVERT: A  133 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6551 (mt-10)
REVERT: B   63 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: C   36 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7705 (mptp)
REVERT: C   55 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8037 (mt)
REVERT: C   95 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7341 (ttpp)
REVERT: C   99 ARG cc_start: 0.7278 (mmm160) cc_final: 0.6894 (mmp-170)
REVERT: C  112 GLN cc_start: 0.6699 (mm-40) cc_final: 0.5758 (mm110)
REVERT: D   43 LYS cc_start: 0.8086 (mptt) cc_final: 0.7072 (mppt)
REVERT: D   68 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6663 (mm-30)
REVERT: D  113 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7527 (ttpt)
REVERT: D  117 LYS cc_start: 0.7869 (tttp) cc_final: 0.7565 (tttt)
REVERT: F   52 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7089 (tp30)
REVERT: F   59 LYS cc_start: 0.7867 (tttp) cc_final: 0.7597 (tppt)
REVERT: F   77 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7299 (mttm)
REVERT: F   79 LYS cc_start: 0.8147 (mttm) cc_final: 0.7383 (mtmt)
REVERT: G   92 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7235 (mt-10)
REVERT: G  101 THR cc_start: 0.8355 (m) cc_final: 0.8024 (m)
REVERT: H   40 LYS cc_start: 0.7788 (mttt) cc_final: 0.7510 (mttm)
REVERT: H   68 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6827 (mp0)
REVERT: H  116 THR cc_start: 0.8031 (m) cc_final: 0.7824 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 126
  average time/residue: 1.9226
  time to fit residues: 254.9819
Evaluate side-chains
  133 residues out of total 625 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   82 LYS
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.174183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140841 restraints weight = 10960.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 0.65
r_work: 0.3308 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12623  Z= 0.235
  Angle     :  0.606   6.272  18274  Z= 0.361
  Chirality :  0.036   0.135   2079
  Planarity :  0.004   0.037   1324
  Dihedral  : 31.223 179.620   3959
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.68 %
    Favored  : 77.92 %
  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:  1.76 (0.30), residues: 737
  helix:  1.86 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.81 (0.36), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.002   PHE D  67 
 TYR   0.013   0.002   TYR H  34 
 ARG   0.006   0.001   ARG A  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4376.38 seconds
wall clock time: 77 minutes 56.20 seconds (4676.20 seconds total)