Starting phenix.real_space_refine
on Wed Mar  4 15:15:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pff_13374/03_2026/7pff_13374.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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     334      5.49       5
     S      10      5.16       5
     C    7085      2.51       5
     N    2430      2.21       5
     O    3076      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12935
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "K"
      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: "L"
      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: "M"
      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: "N"
      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: "O"
      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: "P"
      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: "Q"
      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: "R"
      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: "I"
      Number of atoms: 3407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3407
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "J"
      Number of atoms: 3440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3440
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 3.02, per 1000 atoms: 0.23
  Number of scatterers: 12935
  At special positions: 0
  Unit cell: (128.1, 130.2, 112.35, 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     334     15.00
     O    3076      8.00
     N    2430      7.00
     C    7085      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 475.1 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      70.7% alpha, 2.6% beta
      167 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 2.24
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.741A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE K  78 " --> pdb=" O   ILE K  74 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.774A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.907A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 93
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.399A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 88
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 37 through 49
    Processing helix  chain 'N' and resid 55 through 84
    Processing helix  chain 'N' and resid 90 through 102
    Processing helix  chain 'N' and resid 104 through 123
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 76
      removed outlier: 3.579A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.994A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 29
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 4.060A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.765A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 16 through 22
    Processing helix  chain 'Q' and resid 26 through 37
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.173A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
      removed outlier: 3.536A  pdb=" N   ASN Q  89 " --> pdb=" O   LEU Q  85 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 90 through 97
    Processing helix  chain 'Q' and resid 112 through 116
    Processing helix  chain 'R' and resid 37 through 49
    Processing helix  chain 'R' and resid 55 through 84
    Processing helix  chain 'R' and resid 90 through 102
    Processing helix  chain 'R' and resid 104 through 124
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.933A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.321A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 102
      removed outlier: 6.465A  pdb=" N   THR M 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.779A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.350A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    401 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      427 hydrogen bonds
      854 hydrogen bond angles
      0 basepair planarities
      167 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 3.16

  Time building geometry restraints manager: 1.49 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: 2762
        1.33 -     1.46: 4906
        1.46 -     1.58: 5494
        1.58 -     1.70: 666
        1.70 -     1.83: 20
  Bond restraints: 13848
  Sorted by residual:
  bond pdb=" O3'  DC I 563 "
       pdb=" P    DT I 564 "
    ideal  model  delta    sigma   weight residual
    1.607  1.665 -0.058 1.50e-02 4.44e+03 1.47e+01
  bond pdb=" CB  MET N  59 "
       pdb=" CG  MET N  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 3.96e+00
  bond pdb=" C3'  DG J 316 "
       pdb=" O3'  DG J 316 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 3.00e-02 1.11e+03 3.67e+00
  bond pdb=" C3'  DC J 238 "
       pdb=" O3'  DC J 238 "
    ideal  model  delta    sigma   weight residual
    1.422  1.478 -0.056 3.00e-02 1.11e+03 3.45e+00
  bond pdb=" C3'  DC I 430 "
       pdb=" O3'  DC I 430 "
    ideal  model  delta    sigma   weight residual
    1.422  1.475 -0.053 3.00e-02 1.11e+03 3.14e+00
  ... (remaining 13843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 19164
        2.00 -     4.01: 880
        4.01 -     6.01: 60
        6.01 -     8.02: 24
        8.02 -    10.02: 7
  Bond angle restraints: 20135
  Sorted by residual:
  angle pdb=" O3'  DC I 562 "
        pdb=" C3'  DC I 562 "
        pdb=" C2'  DC I 562 "
      ideal   model   delta    sigma   weight residual
     111.50  120.57   -9.07 1.50e+00 4.44e-01 3.65e+01
  angle pdb=" N   GLU Q  61 "
        pdb=" CA  GLU Q  61 "
        pdb=" CB  GLU Q  61 "
      ideal   model   delta    sigma   weight residual
     110.28  118.22   -7.94 1.55e+00 4.16e-01 2.62e+01
  angle pdb=" N   GLU O  97 "
        pdb=" CA  GLU O  97 "
        pdb=" CB  GLU O  97 "
      ideal   model   delta    sigma   weight residual
     110.28  115.93   -5.65 1.55e+00 4.16e-01 1.33e+01
  angle pdb=" CA  MET N  59 "
        pdb=" CB  MET N  59 "
        pdb=" CG  MET N  59 "
      ideal   model   delta    sigma   weight residual
     114.10  106.93    7.17 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" C3'  DG J 316 "
        pdb=" O3'  DG J 316 "
        pdb=" P    DG J 317 "
      ideal   model   delta    sigma   weight residual
     120.20  125.47   -5.27 1.50e+00 4.44e-01 1.23e+01
  ... (remaining 20130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.49: 5567
       34.49 -    68.98: 1838
       68.98 -   103.47: 55
      103.47 -   137.96: 3
      137.96 -   172.46: 1
  Dihedral angle restraints: 7464
    sinusoidal: 5242
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  PRO R 103 "
           pdb=" C   PRO R 103 "
           pdb=" N   GLY R 104 "
           pdb=" CA  GLY R 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.31   20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ILE L  50 "
           pdb=" C   ILE L  50 "
           pdb=" N   TYR L  51 "
           pdb=" CA  TYR L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.09  -19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" C4'  DG J 316 "
           pdb=" C3'  DG J 316 "
           pdb=" O3'  DG J 316 "
           pdb=" P    DG J 317 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.54  172.46     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1726
       0.053 -    0.106: 475
       0.106 -    0.160: 71
       0.160 -    0.213: 15
       0.213 -    0.266: 1
  Chirality restraints: 2288
  Sorted by residual:
  chirality pdb=" C3'  DC I 562 "
            pdb=" C4'  DC I 562 "
            pdb=" O3'  DC I 562 "
            pdb=" C2'  DC I 562 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.39   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CB  THR P  54 "
            pdb=" CA  THR P  54 "
            pdb=" OG1 THR P  54 "
            pdb=" CG2 THR P  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C4'  DA I 439 "
            pdb=" C5'  DA I 439 "
            pdb=" O4'  DA I 439 "
            pdb=" C3'  DA I 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.32   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 2285 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU R 113 "    0.019 2.00e-02 2.50e+03   3.89e-02 1.51e+01
        pdb=" CD  GLU R 113 "   -0.067 2.00e-02 2.50e+03
        pdb=" OE1 GLU R 113 "    0.024 2.00e-02 2.50e+03
        pdb=" OE2 GLU R 113 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I 560 "    0.047 2.00e-02 2.50e+03   2.08e-02 1.19e+01
        pdb=" N9   DA I 560 "   -0.045 2.00e-02 2.50e+03
        pdb=" C8   DA I 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I 560 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I 560 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DA I 560 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I 560 "    0.016 2.00e-02 2.50e+03
        pdb=" N1   DA I 560 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I 560 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DA I 560 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I 560 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K 104 "    0.013 2.00e-02 2.50e+03   2.00e-02 7.00e+00
        pdb=" CG  PHE K 104 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE K 104 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE K 104 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE K 104 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE K 104 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE K 104 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3108
        2.81 -     3.33: 12445
        3.33 -     3.85: 28738
        3.85 -     4.38: 31734
        4.38 -     4.90: 43238
  Nonbonded interactions: 119263
  Sorted by model distance:
  nonbonded pdb=" O   VAL N 118 "
            pdb=" OG1 THR N 122 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   THR Q  16 "
            pdb=" OG  SER Q  19 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD1 ASP K 123 "
            pdb=" NE2 HIS O 113 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   GLN K  55 "
            pdb=" NH2 ARG Q  81 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH2 ARG M  81 "
            pdb=" O   GLN O  55 "
     model   vdw
     2.311 3.120
  ... (remaining 119258 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 'K'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'R'
}

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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.740
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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   0.060  13848  Z= 0.283
  Angle     :  0.921  10.019  20135  Z= 0.532
  Chirality :  0.050   0.266   2288
  Planarity :  0.007   0.071   1390
  Dihedral  : 30.348 172.456   6032
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.28), residues: 752
  helix:  0.19 (0.21), residues: 510
  sheet:  None (None), residues: 0
  loop : -0.28 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P  95 
 TYR   0.033   0.003   TYR O  54 
 PHE   0.045   0.004   PHE K 104 
 HIS   0.009   0.002   HIS N 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 (13848)
  covalent geometry    : angle       0.92146 (20135)
  hydrogen bonds       : bond        0.11994 (  828)
  hydrogen bonds       : angle       4.62731 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9229 (m-80) cc_final: 0.8907 (m-80)
REVERT: N  109 HIS cc_start: 0.9687 (m-70) cc_final: 0.9380 (m90)
REVERT: O   81 ASP cc_start: 0.9446 (m-30) cc_final: 0.9066 (p0)
REVERT: R  102 LEU cc_start: 0.8679 (tp) cc_final: 0.8386 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0948
  time to fit residues: 12.9634
Evaluate side-chains
  62 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
N 109 HIS
O  76 GLN
R  47 GLN
R 109 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.044515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.032296 restraints weight = 134746.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.033607 restraints weight = 88873.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.034600 restraints weight = 66330.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.035356 restraints weight = 53035.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.035929 restraints weight = 44600.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13848  Z= 0.197
  Angle     :  0.649   5.455  20135  Z= 0.394
  Chirality :  0.037   0.146   2288
  Planarity :  0.005   0.057   1390
  Dihedral  : 33.491 168.847   4508
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.42 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.29), residues: 752
  helix:  0.92 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.08 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.013   0.002   TYR Q  39 
 PHE   0.012   0.001   PHE N  65 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (13848)
  covalent geometry    : angle       0.64918 (20135)
  hydrogen bonds       : bond        0.06134 (  828)
  hydrogen bonds       : angle       3.65818 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1001
  time to fit residues: 12.9704
Evaluate side-chains
  51 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 52 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
M  84 GLN
O  76 GLN
O 108 ASN
O 125 GLN
Q  24 GLN
R  47 GLN
** R 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.034310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.028414 restraints weight = 211838.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.029276 restraints weight = 123325.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.029838 restraints weight = 82975.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.030295 restraints weight = 61718.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.030647 restraints weight = 47762.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  13848  Z= 0.267
  Angle     :  0.707   6.178  20135  Z= 0.420
  Chirality :  0.039   0.150   2288
  Planarity :  0.006   0.063   1390
  Dihedral  : 33.892 170.396   4508
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.20 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.29), residues: 752
  helix:  0.98 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.08 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P  95 
 TYR   0.025   0.002   TYR Q  57 
 PHE   0.017   0.002   PHE O 104 
 HIS   0.006   0.002   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (13848)
  covalent geometry    : angle       0.70700 (20135)
  hydrogen bonds       : bond        0.08712 (  828)
  hydrogen bonds       : angle       3.97973 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9433 (mt) cc_final: 0.9201 (mm)
REVERT: K   54 TYR cc_start: 0.9467 (m-80) cc_final: 0.9081 (m-80)
REVERT: K   94 GLU cc_start: 0.8960 (tp30) cc_final: 0.8723 (tp30)
REVERT: K  104 PHE cc_start: 0.9695 (m-80) cc_final: 0.9362 (m-80)
REVERT: K  108 ASN cc_start: 0.9169 (t0) cc_final: 0.8394 (p0)
REVERT: N  109 HIS cc_start: 0.9499 (m90) cc_final: 0.9103 (m-70)
REVERT: R  102 LEU cc_start: 0.9019 (tp) cc_final: 0.8727 (tp)
REVERT: R  109 HIS cc_start: 0.9716 (m-70) cc_final: 0.9267 (m170)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0980
  time to fit residues: 12.4268
Evaluate side-chains
  56 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
O  76 GLN
O 108 ASN
Q  24 GLN
R  47 GLN
R 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.036280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.030321 restraints weight = 199280.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.031235 restraints weight = 115238.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.031857 restraints weight = 76859.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.032300 restraints weight = 56248.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.032647 restraints weight = 43846.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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      :  0.004   0.041  13848  Z= 0.181
  Angle     :  0.634   6.146  20135  Z= 0.382
  Chirality :  0.037   0.143   2288
  Planarity :  0.004   0.059   1390
  Dihedral  : 33.515 169.672   4508
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 752
  helix:  1.36 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.11 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  86 
 TYR   0.022   0.001   TYR N  42 
 PHE   0.015   0.002   PHE O 104 
 HIS   0.003   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (13848)
  covalent geometry    : angle       0.63359 (20135)
  hydrogen bonds       : bond        0.05057 (  828)
  hydrogen bonds       : angle       3.41654 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9338 (mt) cc_final: 0.9056 (mm)
REVERT: K   54 TYR cc_start: 0.9395 (m-80) cc_final: 0.9046 (m-80)
REVERT: K  104 PHE cc_start: 0.9628 (m-80) cc_final: 0.9359 (m-80)
REVERT: N  108 LYS cc_start: 0.9626 (ptpp) cc_final: 0.9349 (pttm)
REVERT: N  109 HIS cc_start: 0.9445 (m90) cc_final: 0.9041 (m-70)
REVERT: Q   26 PRO cc_start: 0.6933 (Cg_endo) cc_final: 0.6517 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8987 (tp) cc_final: 0.8702 (tp)
REVERT: R  109 HIS cc_start: 0.9603 (m90) cc_final: 0.9116 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0992
  time to fit residues: 12.3600
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 54 optimal weight:    0.3980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.045484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.036349 restraints weight = 175185.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.037378 restraints weight = 103140.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.038097 restraints weight = 72702.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.038607 restraints weight = 55936.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.038976 restraints weight = 46074.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13848  Z= 0.156
  Angle     :  0.604   6.194  20135  Z= 0.363
  Chirality :  0.035   0.136   2288
  Planarity :  0.004   0.055   1390
  Dihedral  : 33.049 166.514   4508
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.89 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.30), residues: 752
  helix:  1.69 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.03 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  35 
 TYR   0.021   0.001   TYR N  42 
 PHE   0.012   0.001   PHE R  65 
 HIS   0.003   0.001   HIS K 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (13848)
  covalent geometry    : angle       0.60429 (20135)
  hydrogen bonds       : bond        0.03925 (  828)
  hydrogen bonds       : angle       3.09994 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.8802 (mt) cc_final: 0.8526 (mm)
REVERT: Q   26 PRO cc_start: 0.7695 (Cg_endo) cc_final: 0.7381 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.6600 (tp) cc_final: 0.6389 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0955
  time to fit residues: 12.5771
Evaluate side-chains
  55 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 109 HIS
O  76 GLN
O 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.035974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.030081 restraints weight = 201502.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.030996 restraints weight = 115487.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.031632 restraints weight = 76717.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.032118 restraints weight = 55944.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.032465 restraints weight = 42799.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13848  Z= 0.187
  Angle     :  0.612   5.894  20135  Z= 0.367
  Chirality :  0.035   0.143   2288
  Planarity :  0.004   0.061   1390
  Dihedral  : 33.270 164.714   4508
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.30), residues: 752
  helix:  1.70 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.15 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  95 
 TYR   0.015   0.001   TYR N  42 
 PHE   0.031   0.002   PHE O 104 
 HIS   0.004   0.001   HIS N 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (13848)
  covalent geometry    : angle       0.61212 (20135)
  hydrogen bonds       : bond        0.05561 (  828)
  hydrogen bonds       : angle       3.33386 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9221 (mt) cc_final: 0.8878 (mm)
REVERT: K   54 TYR cc_start: 0.9491 (m-10) cc_final: 0.9247 (m-80)
REVERT: K  100 LEU cc_start: 0.9805 (mp) cc_final: 0.9570 (mt)
REVERT: K  104 PHE cc_start: 0.9564 (m-10) cc_final: 0.9272 (m-80)
REVERT: Q   26 PRO cc_start: 0.6938 (Cg_endo) cc_final: 0.6491 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8771 (tp) cc_final: 0.8472 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0991
  time to fit residues: 11.7759
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.035115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.028235 restraints weight = 178694.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.029125 restraints weight = 107608.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.029742 restraints weight = 75711.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.030228 restraints weight = 58158.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.030560 restraints weight = 46879.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13848  Z= 0.178
  Angle     :  0.614   5.946  20135  Z= 0.369
  Chirality :  0.035   0.141   2288
  Planarity :  0.004   0.060   1390
  Dihedral  : 33.144 164.174   4508
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.30), residues: 752
  helix:  1.66 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.13 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  67 
 TYR   0.016   0.001   TYR P  72 
 PHE   0.009   0.001   PHE O 104 
 HIS   0.003   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13848)
  covalent geometry    : angle       0.61352 (20135)
  hydrogen bonds       : bond        0.05002 (  828)
  hydrogen bonds       : angle       3.28101 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   51 ILE cc_start: 0.9155 (mt) cc_final: 0.8835 (mm)
REVERT: K   54 TYR cc_start: 0.9438 (m-10) cc_final: 0.9201 (m-80)
REVERT: K  100 LEU cc_start: 0.9809 (mp) cc_final: 0.9500 (mt)
REVERT: K  104 PHE cc_start: 0.9569 (m-10) cc_final: 0.9288 (m-80)
REVERT: N   71 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8571 (mm-30)
REVERT: O   79 LYS cc_start: 0.9292 (mppt) cc_final: 0.8768 (tmtt)
REVERT: Q   26 PRO cc_start: 0.6679 (Cg_endo) cc_final: 0.6216 (Cg_exo)
REVERT: R  102 LEU cc_start: 0.8836 (tp) cc_final: 0.8472 (tp)
REVERT: R  105 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8857 (tm-30)
REVERT: R  109 HIS cc_start: 0.9674 (m90) cc_final: 0.9080 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1050
  time to fit residues: 12.9214
Evaluate side-chains
  63 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  75 HIS
L  93 GLN
N  67 ASN
N  95 GLN
O  55 GLN
O  76 GLN
** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 112 GLN
R  84 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.031795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.026526 restraints weight = 215011.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.027296 restraints weight = 127005.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.027811 restraints weight = 85642.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.028209 restraints weight = 63371.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.028514 restraints weight = 49455.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075  13848  Z= 0.340
  Angle     :  0.762   6.550  20135  Z= 0.449
  Chirality :  0.042   0.176   2288
  Planarity :  0.007   0.065   1390
  Dihedral  : 34.208 163.621   4508
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 27.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.29), residues: 752
  helix:  0.86 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.32 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K  69 
 TYR   0.015   0.003   TYR P  72 
 PHE   0.041   0.003   PHE O 104 
 HIS   0.005   0.001   HIS K  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 (13848)
  covalent geometry    : angle       0.76185 (20135)
  hydrogen bonds       : bond        0.10846 (  828)
  hydrogen bonds       : angle       4.24277 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9485 (m-10) cc_final: 0.9234 (m-10)
REVERT: K  104 PHE cc_start: 0.9713 (m-10) cc_final: 0.9403 (m-80)
REVERT: M   59 THR cc_start: 0.9752 (m) cc_final: 0.9534 (p)
REVERT: N   71 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: O   81 ASP cc_start: 0.9109 (m-30) cc_final: 0.8843 (m-30)
REVERT: Q   26 PRO cc_start: 0.7118 (Cg_endo) cc_final: 0.6716 (Cg_exo)
REVERT: R   94 ILE cc_start: 0.9636 (mm) cc_final: 0.9308 (tt)
REVERT: R  102 LEU cc_start: 0.9019 (tp) cc_final: 0.8672 (tp)
REVERT: R  108 LYS cc_start: 0.9751 (ptpp) cc_final: 0.9550 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1012
  time to fit residues: 11.8445
Evaluate side-chains
  56 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN
** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.033958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.028470 restraints weight = 205317.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.029336 restraints weight = 118207.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.029892 restraints weight = 78628.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.030322 restraints weight = 57791.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.030655 restraints weight = 44737.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13848  Z= 0.204
  Angle     :  0.663   6.203  20135  Z= 0.395
  Chirality :  0.038   0.145   2288
  Planarity :  0.005   0.059   1390
  Dihedral  : 33.717 161.142   4508
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.30), residues: 752
  helix:  1.29 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.33 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  95 
 TYR   0.013   0.001   TYR N  42 
 PHE   0.023   0.002   PHE O 104 
 HIS   0.003   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (13848)
  covalent geometry    : angle       0.66321 (20135)
  hydrogen bonds       : bond        0.06284 (  828)
  hydrogen bonds       : angle       3.63776 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LEU cc_start: 0.9541 (tt) cc_final: 0.9112 (mm)
REVERT: K   51 ILE cc_start: 0.9097 (mt) cc_final: 0.8724 (mm)
REVERT: K   54 TYR cc_start: 0.9425 (m-10) cc_final: 0.9224 (m-80)
REVERT: K  104 PHE cc_start: 0.9597 (m-10) cc_final: 0.9274 (m-80)
REVERT: Q   26 PRO cc_start: 0.6770 (Cg_endo) cc_final: 0.6326 (Cg_exo)
REVERT: R   94 ILE cc_start: 0.9626 (mm) cc_final: 0.9331 (tt)
REVERT: R  102 LEU cc_start: 0.8875 (tp) cc_final: 0.8461 (tp)
REVERT: R  108 LYS cc_start: 0.9730 (ptpp) cc_final: 0.9490 (ptpp)
REVERT: R  109 HIS cc_start: 0.9698 (m90) cc_final: 0.9147 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0886
  time to fit residues: 10.7580
Evaluate side-chains
  60 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 96 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN
** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.034821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.029079 restraints weight = 200140.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.029969 restraints weight = 115803.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.030574 restraints weight = 77885.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.031035 restraints weight = 57036.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.031404 restraints weight = 44018.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13848  Z= 0.180
  Angle     :  0.631   6.511  20135  Z= 0.376
  Chirality :  0.036   0.141   2288
  Planarity :  0.004   0.059   1390
  Dihedral  : 33.355 157.790   4508
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.30), residues: 752
  helix:  1.59 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.33 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  69 
 TYR   0.013   0.001   TYR N  42 
 PHE   0.023   0.001   PHE O 104 
 HIS   0.003   0.001   HIS O  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (13848)
  covalent geometry    : angle       0.63148 (20135)
  hydrogen bonds       : bond        0.05092 (  828)
  hydrogen bonds       : angle       3.41475 ( 2045)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LEU cc_start: 0.9543 (tt) cc_final: 0.9228 (pp)
REVERT: K  100 LEU cc_start: 0.9813 (mp) cc_final: 0.9554 (mt)
REVERT: K  104 PHE cc_start: 0.9470 (m-10) cc_final: 0.9175 (m-80)
REVERT: N  105 GLU cc_start: 0.9634 (pm20) cc_final: 0.9432 (pm20)
REVERT: O   54 TYR cc_start: 0.8744 (m-10) cc_final: 0.8495 (m-80)
REVERT: O   80 THR cc_start: 0.9150 (p) cc_final: 0.8917 (p)
REVERT: O  104 PHE cc_start: 0.9384 (m-80) cc_final: 0.9181 (m-80)
REVERT: Q   26 PRO cc_start: 0.6664 (Cg_endo) cc_final: 0.6187 (Cg_exo)
REVERT: R   94 ILE cc_start: 0.9620 (mm) cc_final: 0.9335 (tt)
REVERT: R  102 LEU cc_start: 0.8704 (tp) cc_final: 0.8302 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0953
  time to fit residues: 11.9057
Evaluate side-chains
  61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** L  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN
** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.034765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.029031 restraints weight = 199661.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.029941 restraints weight = 115339.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.030538 restraints weight = 77137.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.031031 restraints weight = 56813.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.031385 restraints weight = 43612.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.6280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13848  Z= 0.181
  Angle     :  0.636   9.075  20135  Z= 0.377
  Chirality :  0.036   0.143   2288
  Planarity :  0.004   0.057   1390
  Dihedral  : 33.358 156.079   4508
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.30), residues: 752
  helix:  1.61 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.32 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  72 
 TYR   0.011   0.001   TYR R  37 
 PHE   0.024   0.002   PHE O 104 
 HIS   0.003   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (13848)
  covalent geometry    : angle       0.63558 (20135)
  hydrogen bonds       : bond        0.05207 (  828)
  hydrogen bonds       : angle       3.37729 ( 2045)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1770.42 seconds
wall clock time: 31 minutes 28.05 seconds (1888.05 seconds total)