Starting phenix.real_space_refine
on Fri Jul  3 13:58:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pf4_13367/07_2026/7pf4_13367.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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    7084      2.51       5
     N    2431      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 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: "J"
      Number of atoms: 3442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3442
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
    Chain: "I"
      Number of atoms: 3405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3405
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 2.68, per 1000 atoms: 0.21
  Number of scatterers: 12935
  At special positions: 0
  Unit cell: (116.55, 152.25, 117.6, 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    2431      7.00
     C    7084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 532.0 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 8 sheets defined
      71.1% alpha, 2.1% beta
      165 base pairs and 285 stacking pairs defined.
    Time for finding SS restraints: 2.04
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.711A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 3.614A  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: 3.781A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 3.992A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 4.207A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 94
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 36
      removed outlier: 3.668A  pdb=" N   VAL M  30 " --> pdb=" O   PRO M  26 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.053A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 37 through 49
      removed outlier: 3.550A  pdb=" N   VAL N  41 " --> pdb=" O   TYR N  37 " (cutoff:3.500A)
    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 79
      removed outlier: 3.764A  pdb=" N   PHE O  78 " --> pdb=" O   ILE O  74 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
    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: 3.759A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
    Processing helix  chain 'Q' and resid 16 through 21
    Processing helix  chain 'Q' and resid 26 through 36
      removed outlier: 3.669A  pdb=" N   VAL Q  30 " --> pdb=" O   PRO Q  26 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.285A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
    Processing helix  chain 'Q' and resid 90 through 97
    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 103 through 123
      removed outlier: 3.695A  pdb=" N   ALA R 107 " --> pdb=" O   PRO R 103 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS R 108 " --> pdb=" O   GLY R 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.735A  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 'M' and resid 42 through 43
      removed outlier: 7.229A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.675A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.181A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 77 through 78

    399 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      423 hydrogen bonds
      846 hydrogen bond angles
      0 basepair planarities
      165 basepair parallelities
      285 stacking parallelities
  Total time for adding SS restraints: 3.04

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2644
        1.34 -     1.46: 4652
        1.46 -     1.58: 5866
        1.58 -     1.70: 666
        1.70 -     1.82: 20
  Bond restraints: 13848
  Sorted by residual:
  bond pdb=" C5'  DA I 453 "
       pdb=" C4'  DA I 453 "
    ideal  model  delta    sigma   weight residual
    1.512  1.542 -0.030 7.00e-03 2.04e+04 1.79e+01
  bond pdb=" C3'  DG I 522 "
       pdb=" O3'  DG I 522 "
    ideal  model  delta    sigma   weight residual
    1.435  1.485 -0.050 1.30e-02 5.92e+03 1.45e+01
  bond pdb=" C5'  DA I 433 "
       pdb=" C4'  DA I 433 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.33e+01
  bond pdb=" C3'  DG I 410 "
       pdb=" O3'  DG I 410 "
    ideal  model  delta    sigma   weight residual
    1.435  1.481 -0.046 1.30e-02 5.92e+03 1.24e+01
  bond pdb=" C5'  DA I 525 "
       pdb=" C4'  DA I 525 "
    ideal  model  delta    sigma   weight residual
    1.512  1.536 -0.024 7.00e-03 2.04e+04 1.14e+01
  ... (remaining 13843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 19541
        2.52 -     5.03: 535
        5.03 -     7.55: 47
        7.55 -    10.06: 10
       10.06 -    12.58: 2
  Bond angle restraints: 20135
  Sorted by residual:
  angle pdb=" CA  GLU K  97 "
        pdb=" CB  GLU K  97 "
        pdb=" CG  GLU K  97 "
      ideal   model   delta    sigma   weight residual
     114.10  126.68  -12.58 2.00e+00 2.50e-01 3.95e+01
  angle pdb=" C   ILE M  87 "
        pdb=" N   ARG M  88 "
        pdb=" CA  ARG M  88 "
      ideal   model   delta    sigma   weight residual
     122.73  112.87    9.86 1.61e+00 3.86e-01 3.75e+01
  angle pdb=" O4'  DG J 308 "
        pdb=" C1'  DG J 308 "
        pdb=" N9   DG J 308 "
      ideal   model   delta    sigma   weight residual
     108.00  112.01   -4.01 7.00e-01 2.04e+00 3.29e+01
  angle pdb=" O4'  DG J 354 "
        pdb=" C1'  DG J 354 "
        pdb=" N9   DG J 354 "
      ideal   model   delta    sigma   weight residual
     108.00  112.01   -4.01 7.00e-01 2.04e+00 3.28e+01
  angle pdb=" O4'  DT J 295 "
        pdb=" C4'  DT J 295 "
        pdb=" C3'  DT J 295 "
      ideal   model   delta    sigma   weight residual
     106.00  102.57    3.43 6.00e-01 2.78e+00 3.27e+01
  ... (remaining 20130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.22: 5688
       35.22 -    70.44: 1736
       70.44 -   105.66: 33
      105.66 -   140.88: 2
      140.88 -   176.09: 1
  Dihedral angle restraints: 7460
    sinusoidal: 5238
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  ARG L  23 "
           pdb=" C   ARG L  23 "
           pdb=" N   ASP L  24 "
           pdb=" CA  ASP L  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.36  -30.64     0      5.00e+00 4.00e-02 3.76e+01
  dihedral pdb=" CA  ARG M  88 "
           pdb=" C   ARG M  88 "
           pdb=" N   ASN M  89 "
           pdb=" CA  ASN M  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  PRO M  26 "
           pdb=" C   PRO M  26 "
           pdb=" N   VAL M  27 "
           pdb=" CA  VAL M  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 7457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1662
       0.051 -    0.102: 522
       0.102 -    0.153: 78
       0.153 -    0.205: 19
       0.205 -    0.256: 7
  Chirality restraints: 2288
  Sorted by residual:
  chirality pdb=" CA  GLU K  97 "
            pdb=" N   GLU K  97 "
            pdb=" C   GLU K  97 "
            pdb=" CB  GLU K  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  PHE K 104 "
            pdb=" N   PHE K 104 "
            pdb=" C   PHE K 104 "
            pdb=" CB  PHE K 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CG  LEU N  45 "
            pdb=" CB  LEU N  45 "
            pdb=" CD1 LEU N  45 "
            pdb=" CD2 LEU N  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 2285 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE M  25 "    0.065 5.00e-02 4.00e+02   9.96e-02 1.59e+01
        pdb=" N   PRO M  26 "   -0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO M  26 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO M  26 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M  79 "   -0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO M  80 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO M  80 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO M  80 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS N  85 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   LYS N  85 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LYS N  85 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG N  86 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2610
        2.79 -     3.31: 11699
        3.31 -     3.84: 27751
        3.84 -     4.37: 30869
        4.37 -     4.90: 42548
  Nonbonded interactions: 115477
  Sorted by model distance:
  nonbonded pdb=" O   THR M  76 "
            pdb=" OG1 THR N  52 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG L  78 "
            pdb=" O   THR L  80 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" N   GLY Q  44 "
            pdb=" O   ILE R  89 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OH  TYR Q  39 "
            pdb=" OE1 GLU R  71 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" N   GLY M  44 "
            pdb=" O   ILE N  89 "
     model   vdw
     2.336 3.120
  ... (remaining 115472 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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  13848  Z= 0.578
  Angle     :  1.021  12.577  20135  Z= 0.820
  Chirality :  0.051   0.256   2288
  Planarity :  0.007   0.100   1390
  Dihedral  : 29.722 176.094   6028
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.80 (0.27), residues: 752
  helix: -0.21 (0.20), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.02 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG P  45 
 TYR   0.038   0.003   TYR O  99 
 PHE   0.021   0.003   PHE N  65 
 HIS   0.008   0.002   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00663 /  0.58 (13848)
  covalent geometry    : angle       1.02063 /  0.82 (20135)
  hydrogen bonds       : bond        0.09572 /  6.31 (  822)
  hydrogen bonds       : angle       4.76338 /  3.34 ( 2034)

*********************** 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
  168 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  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   94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: K   96 SER cc_start: 0.9070 (m) cc_final: 0.8859 (p)
REVERT: K   99 TYR cc_start: 0.8859 (t80) cc_final: 0.8502 (t80)
REVERT: K  106 ASP cc_start: 0.8751 (m-30) cc_final: 0.8529 (m-30)
REVERT: L   49 LEU cc_start: 0.8979 (mp) cc_final: 0.8723 (mp)
REVERT: M   25 PHE cc_start: 0.7803 (m-80) cc_final: 0.7570 (m-10)
REVERT: N   52 THR cc_start: 0.8016 (t) cc_final: 0.7471 (t)
REVERT: N   71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8272 (tt0)
REVERT: N   95 GLN cc_start: 0.8630 (pp30) cc_final: 0.8074 (tm-30)
REVERT: N  105 GLU cc_start: 0.7939 (tp30) cc_final: 0.7627 (tp30)
REVERT: N  108 LYS cc_start: 0.9269 (ptmm) cc_final: 0.8529 (ptmm)
REVERT: N  116 LYS cc_start: 0.9457 (tmmt) cc_final: 0.8431 (tmtt)
REVERT: O   97 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: Q   79 ILE cc_start: 0.8482 (mm) cc_final: 0.7912 (pt)
REVERT: R   51 ASP cc_start: 0.8340 (p0) cc_final: 0.8092 (p0)
REVERT: R   95 GLN cc_start: 0.8624 (tm130) cc_final: 0.8363 (tm-30)
REVERT: R  102 LEU cc_start: 0.9333 (mt) cc_final: 0.9091 (mp)
REVERT: R  105 GLU cc_start: 0.8324 (mp0) cc_final: 0.7884 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1136
  time to fit residues: 27.2905
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 HIS
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
O  93 GLN
R  47 GLN
R  82 HIS
** R  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.063816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.052034 restraints weight = 118333.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.053188 restraints weight = 68225.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.053947 restraints weight = 47150.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.054369 restraints weight = 36519.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.054711 restraints weight = 31498.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13848  Z= 0.168
  Angle     :  0.761  10.944  20135  Z= 0.438
  Chirality :  0.050   0.300   2288
  Planarity :  0.006   0.067   1390
  Dihedral  : 32.953 178.988   4504
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.91 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.28), residues: 752
  helix:  0.54 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.73 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P  45 
 TYR   0.033   0.002   TYR P  88 
 PHE   0.012   0.002   PHE P  61 
 HIS   0.011   0.002   HIS O 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.17 (13848)
  covalent geometry    : angle       0.76135 /  0.44 (20135)
  hydrogen bonds       : bond        0.05237 /  3.54 (  822)
  hydrogen bonds       : angle       3.70315 /  2.60 ( 2034)

*********************** 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
  147 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   80 THR cc_start: 0.9272 (t) cc_final: 0.9063 (p)
REVERT: K  100 LEU cc_start: 0.9254 (mt) cc_final: 0.8545 (mm)
REVERT: K  104 PHE cc_start: 0.9226 (m-10) cc_final: 0.8679 (m-80)
REVERT: K  105 GLU cc_start: 0.8812 (mp0) cc_final: 0.8536 (mp0)
REVERT: L   59 LYS cc_start: 0.8987 (tppt) cc_final: 0.8728 (tppp)
REVERT: N   85 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8981 (ttpp)
REVERT: N   91 SER cc_start: 0.8499 (p) cc_final: 0.8147 (p)
REVERT: N   95 GLN cc_start: 0.8480 (pp30) cc_final: 0.7889 (tm-30)
REVERT: N   99 ARG cc_start: 0.8737 (ttm110) cc_final: 0.8454 (mtt180)
REVERT: N  108 LYS cc_start: 0.9348 (ptmm) cc_final: 0.8598 (ptmm)
REVERT: O   59 GLU cc_start: 0.8508 (pm20) cc_final: 0.8302 (pm20)
REVERT: R   51 ASP cc_start: 0.8147 (p0) cc_final: 0.7920 (p0)
REVERT: R  108 LYS cc_start: 0.9403 (mtmt) cc_final: 0.9181 (mtmm)
  outliers start: 7
  outliers final: 3
  residues processed: 144
  average time/residue: 0.1087
  time to fit residues: 22.3513
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 52 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 93 optimal weight:   30.0000
   chunk 17 optimal weight:    0.0050
   chunk 63 optimal weight:    3.9990
   chunk 97 optimal weight:   30.0000
   chunk 9 optimal weight:    0.0870
   chunk 81 optimal weight:   30.0000
   overall best weight:    0.3972

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 HIS
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  84 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 = 0.3888 r_free = 0.3888 target = 0.064045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.052239 restraints weight = 118379.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.053411 restraints weight = 68135.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.054151 restraints weight = 46839.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.054684 restraints weight = 36565.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.055091 restraints weight = 30736.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13848  Z= 0.154
  Angle     :  0.703   9.342  20135  Z= 0.409
  Chirality :  0.047   0.267   2288
  Planarity :  0.005   0.064   1390
  Dihedral  : 32.869 176.657   4504
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.16 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.53 (0.29), residues: 752
  helix:  0.85 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  45 
 TYR   0.028   0.002   TYR P  88 
 PHE   0.018   0.002   PHE O  67 
 HIS   0.008   0.002   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.15 (13848)
  covalent geometry    : angle       0.70263 /  0.41 (20135)
  hydrogen bonds       : bond        0.04617 /  3.09 (  822)
  hydrogen bonds       : angle       3.47091 /  2.44 ( 2034)

*********************** 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
  142 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  104 PHE cc_start: 0.9184 (m-10) cc_final: 0.8657 (m-80)
REVERT: K  105 GLU cc_start: 0.8742 (mp0) cc_final: 0.8497 (mp0)
REVERT: K  125 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (mp10)
REVERT: L   59 LYS cc_start: 0.9027 (tppt) cc_final: 0.8798 (tppp)
REVERT: N   91 SER cc_start: 0.8438 (p) cc_final: 0.8178 (p)
REVERT: N   95 GLN cc_start: 0.8539 (pp30) cc_final: 0.7340 (tm-30)
REVERT: N   99 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8330 (mtm-85)
REVERT: N  111 VAL cc_start: 0.9056 (t) cc_final: 0.8686 (p)
REVERT: N  120 LYS cc_start: 0.9343 (mmtp) cc_final: 0.9133 (mmtp)
REVERT: O  104 PHE cc_start: 0.9050 (m-10) cc_final: 0.8721 (m-10)
REVERT: P   79 LYS cc_start: 0.8059 (tppt) cc_final: 0.7595 (tppt)
REVERT: R   35 GLU cc_start: 0.7700 (tp30) cc_final: 0.7426 (tp30)
REVERT: R   51 ASP cc_start: 0.8136 (p0) cc_final: 0.7907 (p0)
REVERT: R  108 LYS cc_start: 0.9414 (mtmt) cc_final: 0.9181 (mtmm)
  outliers start: 10
  outliers final: 7
  residues processed: 136
  average time/residue: 0.1037
  time to fit residues: 20.7930
Evaluate side-chains
  125 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   48 LEU
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
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:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 99 optimal weight:   20.0000
   chunk 73 optimal weight:   30.0000
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 87 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 109 HIS
O  55 GLN
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.062439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.050550 restraints weight = 119459.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.051717 restraints weight = 69552.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.052430 restraints weight = 47874.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.052960 restraints weight = 37528.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.053350 restraints weight = 31538.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13848  Z= 0.174
  Angle     :  0.705  11.626  20135  Z= 0.405
  Chirality :  0.047   0.402   2288
  Planarity :  0.005   0.065   1390
  Dihedral  : 32.865 175.859   4504
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.05 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.29), residues: 752
  helix:  1.15 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.86 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M  77 
 TYR   0.034   0.002   TYR P  88 
 PHE   0.019   0.002   PHE P  61 
 HIS   0.015   0.002   HIS N 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.17 (13848)
  covalent geometry    : angle       0.70461 /  0.41 (20135)
  hydrogen bonds       : bond        0.05666 /  3.83 (  822)
  hydrogen bonds       : angle       3.43715 /  2.42 ( 2034)

*********************** 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
  132 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8247 (mm-30)
REVERT: K  104 PHE cc_start: 0.9191 (m-10) cc_final: 0.8735 (m-80)
REVERT: K  105 GLU cc_start: 0.8831 (mp0) cc_final: 0.8591 (mp0)
REVERT: L   59 LYS cc_start: 0.9123 (tppt) cc_final: 0.8840 (tppp)
REVERT: M   57 TYR cc_start: 0.8808 (t80) cc_final: 0.8590 (t80)
REVERT: N   85 LYS cc_start: 0.9383 (ttpt) cc_final: 0.8989 (ttpp)
REVERT: N   95 GLN cc_start: 0.8668 (pp30) cc_final: 0.8186 (tm-30)
REVERT: N  105 GLU cc_start: 0.8287 (tp30) cc_final: 0.7984 (tp30)
REVERT: N  111 VAL cc_start: 0.9132 (t) cc_final: 0.8811 (p)
REVERT: O   54 TYR cc_start: 0.8631 (m-80) cc_final: 0.8268 (m-80)
REVERT: O  104 PHE cc_start: 0.9095 (m-10) cc_final: 0.8688 (m-10)
REVERT: P   79 LYS cc_start: 0.8340 (tppt) cc_final: 0.7927 (tppt)
REVERT: R  108 LYS cc_start: 0.9463 (mtmt) cc_final: 0.9212 (mtmm)
  outliers start: 11
  outliers final: 7
  residues processed: 128
  average time/residue: 0.0961
  time to fit residues: 18.1221
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   48 LEU
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.061722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.049803 restraints weight = 120785.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.050928 restraints weight = 70278.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.051636 restraints weight = 48898.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.052139 restraints weight = 38339.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.052349 restraints weight = 32476.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13848  Z= 0.188
  Angle     :  0.714  13.486  20135  Z= 0.410
  Chirality :  0.046   0.341   2288
  Planarity :  0.005   0.067   1390
  Dihedral  : 32.917 175.016   4504
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 16.35 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.85 (0.30), residues: 752
  helix:  1.13 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.84 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  40 
 TYR   0.034   0.002   TYR P  88 
 PHE   0.025   0.002   PHE P  61 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.19 (13848)
  covalent geometry    : angle       0.71389 /  0.41 (20135)
  hydrogen bonds       : bond        0.05749 /  3.89 (  822)
  hydrogen bonds       : angle       3.51337 /  2.47 ( 2034)

*********************** 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
  123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8307 (mm-30)
REVERT: K  104 PHE cc_start: 0.9180 (m-10) cc_final: 0.8663 (m-10)
REVERT: M   57 TYR cc_start: 0.8899 (t80) cc_final: 0.8691 (t80)
REVERT: M   61 GLU cc_start: 0.9039 (tp30) cc_final: 0.8822 (tp30)
REVERT: M   89 ASN cc_start: 0.8734 (m-40) cc_final: 0.8511 (m-40)
REVERT: N   95 GLN cc_start: 0.8638 (pp30) cc_final: 0.8184 (tm-30)
REVERT: N  111 VAL cc_start: 0.9073 (t) cc_final: 0.8741 (p)
REVERT: N  120 LYS cc_start: 0.9405 (mmtp) cc_final: 0.9157 (mmtt)
REVERT: O   54 TYR cc_start: 0.8617 (m-80) cc_final: 0.8305 (m-80)
REVERT: O  104 PHE cc_start: 0.9072 (m-10) cc_final: 0.8655 (m-10)
REVERT: R  108 LYS cc_start: 0.9419 (mtmt) cc_final: 0.9174 (mtmm)
  outliers start: 10
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0954
  time to fit residues: 16.9249
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   48 LEU
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:   30.0000
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 74 optimal weight:   30.0000
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.061971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.050084 restraints weight = 119294.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.051226 restraints weight = 69325.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.051922 restraints weight = 47919.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.052423 restraints weight = 37667.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.052769 restraints weight = 31893.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13848  Z= 0.161
  Angle     :  0.704  13.288  20135  Z= 0.400
  Chirality :  0.046   0.354   2288
  Planarity :  0.005   0.064   1390
  Dihedral  : 32.896 174.678   4504
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.98 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.97 (0.30), residues: 752
  helix:  1.19 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.73 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  86 
 TYR   0.023   0.002   TYR P  88 
 PHE   0.020   0.002   PHE P  61 
 HIS   0.006   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 (13848)
  covalent geometry    : angle       0.70369 /  0.40 (20135)
  hydrogen bonds       : bond        0.04972 /  3.34 (  822)
  hydrogen bonds       : angle       3.43022 /  2.42 ( 2034)

*********************** 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
  128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  104 PHE cc_start: 0.9150 (m-10) cc_final: 0.8674 (m-10)
REVERT: M   57 TYR cc_start: 0.8893 (t80) cc_final: 0.8647 (t80)
REVERT: N   95 GLN cc_start: 0.8705 (pp30) cc_final: 0.8343 (pp30)
REVERT: N  109 HIS cc_start: 0.9225 (m170) cc_final: 0.8602 (m170)
REVERT: O   54 TYR cc_start: 0.8642 (m-80) cc_final: 0.8343 (m-80)
REVERT: O  104 PHE cc_start: 0.9066 (m-10) cc_final: 0.8707 (m-10)
REVERT: P   63 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8472 (mm-30)
REVERT: R  108 LYS cc_start: 0.9442 (mtmt) cc_final: 0.9198 (mtmm)
  outliers start: 12
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0950
  time to fit residues: 17.1837
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue   87 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   48 LEU
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   chunk 21 optimal weight:    0.8980
   chunk 80 optimal weight:   20.0000
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 84 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  89 ASN
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 108 ASN
** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.062064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.050173 restraints weight = 119622.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.051319 restraints weight = 69589.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.052032 restraints weight = 47991.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.052525 restraints weight = 37600.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.052775 restraints weight = 31767.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13848  Z= 0.158
  Angle     :  0.703  13.836  20135  Z= 0.399
  Chirality :  0.045   0.257   2288
  Planarity :  0.005   0.064   1390
  Dihedral  : 32.835 174.389   4504
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.45 %
    Favored  : 80.50 %
  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:  0.92 (0.30), residues: 752
  helix:  1.15 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.74 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  53 
 TYR   0.019   0.002   TYR P  88 
 PHE   0.031   0.002   PHE P  61 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.16 (13848)
  covalent geometry    : angle       0.70320 /  0.40 (20135)
  hydrogen bonds       : bond        0.04865 /  3.26 (  822)
  hydrogen bonds       : angle       3.42211 /  2.42 ( 2034)

*********************** 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
  133 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  100 LEU cc_start: 0.9430 (mt) cc_final: 0.8977 (mm)
REVERT: K  104 PHE cc_start: 0.9098 (m-10) cc_final: 0.8745 (m-10)
REVERT: K  105 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8358 (mp0)
REVERT: M   57 TYR cc_start: 0.8862 (t80) cc_final: 0.8634 (t80)
REVERT: N   95 GLN cc_start: 0.8664 (pp30) cc_final: 0.8281 (pp30)
REVERT: N  109 HIS cc_start: 0.9164 (m170) cc_final: 0.8553 (m170)
REVERT: N  111 VAL cc_start: 0.9048 (t) cc_final: 0.8596 (p)
REVERT: N  116 LYS cc_start: 0.9380 (tmtt) cc_final: 0.8816 (tmtt)
REVERT: N  120 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9041 (mmtm)
REVERT: O   54 TYR cc_start: 0.8574 (m-80) cc_final: 0.8290 (m-80)
REVERT: O  104 PHE cc_start: 0.9067 (m-10) cc_final: 0.8667 (m-10)
REVERT: R   35 GLU cc_start: 0.7719 (tp30) cc_final: 0.7495 (tp30)
REVERT: R  105 GLU cc_start: 0.8012 (mp0) cc_final: 0.7783 (mp0)
REVERT: R  108 LYS cc_start: 0.9397 (mtmt) cc_final: 0.9141 (mtmm)
  outliers start: 13
  outliers final: 11
  residues processed: 126
  average time/residue: 0.0977
  time to fit residues: 18.4812
Evaluate side-chains
  123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  126 LEU
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   48 LEU
Chi-restraints excluded: chain O residue  108 ASN
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 88 optimal weight:   40.0000
   chunk 53 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:   30.0000
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.057850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.046056 restraints weight = 104299.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.047127 restraints weight = 61205.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.047862 restraints weight = 43050.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.048356 restraints weight = 33382.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.048671 restraints weight = 28066.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3056

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= 0.204
  Angle     :  0.723  13.414  20135  Z= 0.412
  Chirality :  0.045   0.249   2288
  Planarity :  0.005   0.066   1390
  Dihedral  : 32.888 174.967   4504
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.34 %
    Favored  : 78.77 %
  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:  0.79 (0.29), residues: 752
  helix:  1.03 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.73 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R  86 
 TYR   0.015   0.002   TYR P  88 
 PHE   0.042   0.003   PHE P  61 
 HIS   0.007   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.20 (13848)
  covalent geometry    : angle       0.72323 /  0.41 (20135)
  hydrogen bonds       : bond        0.06443 /  4.38 (  822)
  hydrogen bonds       : angle       3.61203 /  2.56 ( 2034)

*********************** 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
  120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  104 PHE cc_start: 0.9222 (m-10) cc_final: 0.8834 (m-10)
REVERT: K  105 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8475 (mp0)
REVERT: M   57 TYR cc_start: 0.8900 (t80) cc_final: 0.8692 (t80)
REVERT: N   95 GLN cc_start: 0.8824 (pp30) cc_final: 0.8444 (pp30)
REVERT: N  109 HIS cc_start: 0.9257 (m170) cc_final: 0.8657 (m170)
REVERT: N  111 VAL cc_start: 0.9234 (t) cc_final: 0.8889 (p)
REVERT: O   54 TYR cc_start: 0.8679 (m-80) cc_final: 0.8392 (m-80)
REVERT: O   93 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7782 (tp40)
REVERT: O  104 PHE cc_start: 0.9174 (m-10) cc_final: 0.8746 (m-10)
REVERT: P   63 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8464 (mm-30)
REVERT: R  108 LYS cc_start: 0.9482 (mtmt) cc_final: 0.9213 (mtmm)
  outliers start: 12
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0964
  time to fit residues: 16.8000
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   82 LEU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  126 LEU
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain O residue   93 GLN
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   44 VAL
Chi-restraints excluded: chain R residue   48 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 103 optimal weight:   30.0000
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.061188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.049343 restraints weight = 120431.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.050470 restraints weight = 69127.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.051172 restraints weight = 47853.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.051607 restraints weight = 37424.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.051947 restraints weight = 32238.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13848  Z= 0.164
  Angle     :  0.709  13.374  20135  Z= 0.404
  Chirality :  0.045   0.267   2288
  Planarity :  0.005   0.064   1390
  Dihedral  : 32.918 175.151   4504
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.97 %
    Favored  : 78.30 %
  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:  0.74 (0.30), residues: 752
  helix:  0.97 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.68 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  86 
 TYR   0.015   0.002   TYR R  40 
 PHE   0.038   0.002   PHE P  61 
 HIS   0.006   0.001   HIS N  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.16 (13848)
  covalent geometry    : angle       0.70936 /  0.40 (20135)
  hydrogen bonds       : bond        0.04935 /  3.32 (  822)
  hydrogen bonds       : angle       3.53586 /  2.50 ( 2034)

*********************** 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
  125 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  104 PHE cc_start: 0.9120 (m-10) cc_final: 0.8785 (m-10)
REVERT: K  105 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8327 (mp0)
REVERT: L   44 LYS cc_start: 0.8328 (mmpt) cc_final: 0.8051 (mmmt)
REVERT: M   57 TYR cc_start: 0.8902 (t80) cc_final: 0.8672 (t80)
REVERT: N   95 GLN cc_start: 0.8713 (pp30) cc_final: 0.8321 (pp30)
REVERT: N  109 HIS cc_start: 0.9155 (m170) cc_final: 0.8589 (m170)
REVERT: N  111 VAL cc_start: 0.9172 (t) cc_final: 0.8812 (p)
REVERT: O   54 TYR cc_start: 0.8629 (m-80) cc_final: 0.8354 (m-80)
REVERT: O  104 PHE cc_start: 0.9158 (m-10) cc_final: 0.8645 (m-10)
REVERT: R   35 GLU cc_start: 0.7817 (tp30) cc_final: 0.7379 (tp30)
REVERT: R  108 LYS cc_start: 0.9405 (mtmt) cc_final: 0.9148 (mtmm)
  outliers start: 11
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0995
  time to fit residues: 17.6575
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  126 LEU
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 93 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 96 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  39 HIS
O  93 GLN
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.061791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.049956 restraints weight = 119519.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.051109 restraints weight = 69397.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.051822 restraints weight = 47923.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.052289 restraints weight = 37474.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.052642 restraints weight = 31895.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  13848  Z= 0.155
  Angle     :  0.716  14.706  20135  Z= 0.405
  Chirality :  0.045   0.260   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 32.813 174.411   4504
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.44 %
    Favored  : 77.67 %
  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:  0.75 (0.30), residues: 752
  helix:  1.02 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.77 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG M  20 
 TYR   0.015   0.002   TYR Q  57 
 PHE   0.027   0.002   PHE P  61 
 HIS   0.006   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.15 (13848)
  covalent geometry    : angle       0.71637 /  0.41 (20135)
  hydrogen bonds       : bond        0.04601 /  3.05 (  822)
  hydrogen bonds       : angle       3.49350 /  2.47 ( 2034)

********************** 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
  127 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  100 LEU cc_start: 0.9442 (mt) cc_final: 0.8971 (mm)
REVERT: K  104 PHE cc_start: 0.9098 (m-10) cc_final: 0.8739 (m-10)
REVERT: K  105 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8300 (mp0)
REVERT: M   57 TYR cc_start: 0.8906 (t80) cc_final: 0.8691 (t80)
REVERT: M   89 ASN cc_start: 0.8649 (m-40) cc_final: 0.8444 (m-40)
REVERT: N   95 GLN cc_start: 0.8685 (pp30) cc_final: 0.8304 (pp30)
REVERT: N  109 HIS cc_start: 0.9163 (m170) cc_final: 0.8588 (m170)
REVERT: N  111 VAL cc_start: 0.9144 (t) cc_final: 0.8787 (p)
REVERT: O   54 TYR cc_start: 0.8567 (m-80) cc_final: 0.8348 (m-80)
REVERT: O  104 PHE cc_start: 0.9122 (m-10) cc_final: 0.8650 (m-10)
REVERT: R   35 GLU cc_start: 0.8126 (tp30) cc_final: 0.7626 (tp30)
REVERT: R  108 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9161 (mtmm)
  outliers start: 12
  outliers final: 11
  residues processed: 123
  average time/residue: 0.0814
  time to fit residues: 15.0936
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   97 GLU
Chi-restraints excluded: chain K residue  125 GLN
Chi-restraints excluded: chain K residue  126 LEU
Chi-restraints excluded: chain M residue   87 ILE
Chi-restraints excluded: chain M residue  114 VAL
Chi-restraints excluded: chain N residue  108 LYS
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   68 ASP
Chi-restraints excluded: chain Q residue   16 THR
Chi-restraints excluded: chain R residue   42 TYR
Chi-restraints excluded: chain R residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:   30.0000
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 8 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    1.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.061041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.049297 restraints weight = 119590.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.050428 restraints weight = 69733.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.051132 restraints weight = 48327.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.051577 restraints weight = 37769.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.051967 restraints weight = 32358.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  13848  Z= 0.173
  Angle     :  0.736  16.823  20135  Z= 0.411
  Chirality :  0.044   0.262   2288
  Planarity :  0.005   0.063   1390
  Dihedral  : 32.797 174.033   4504
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 19.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.07 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.78 (0.30), residues: 752
  helix:  1.04 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.78 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  69 
 TYR   0.016   0.002   TYR K  99 
 PHE   0.055   0.003   PHE P  61 
 HIS   0.007   0.001   HIS R 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.17 (13848)
  covalent geometry    : angle       0.73579 /  0.41 (20135)
  hydrogen bonds       : bond        0.05389 /  3.65 (  822)
  hydrogen bonds       : angle       3.52306 /  2.50 ( 2034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1930.62 seconds
wall clock time: 34 minutes 6.23 seconds (2046.23 seconds total)