Starting phenix.real_space_refine
on Sat Aug 23 12:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl9_36389/08_2025/8jl9_36389.map"
  }
  resolution = 2.65
  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=   0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     310      5.49       5
     S      14      5.16       5
     C    6763      2.51       5
     N    2312      2.21       5
     O    2915      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12314
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3178
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
    Chain: "J"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3177
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
  Time building chain proxies: 3.59, per 1000 atoms: 0.29
  Number of scatterers: 12314
  At special positions: 0
  Unit cell: (74.2, 120.84, 129.32, 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      14     16.00
     P     310     15.00
     O    2915      8.00
     N    2312      7.00
     C    6763      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 446.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 3.2% beta
      155 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 2.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.932A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.656A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.481A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.504A  pdb=" N   LEU C 116 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.973A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.671A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.474A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.897A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.277A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.329A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.914A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.126A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    412 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      398 hydrogen bonds
      796 hydrogen bond angles
      0 basepair planarities
      155 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 2.94

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2146
        1.33 -     1.45: 4427
        1.45 -     1.57: 5950
        1.57 -     1.69: 619
        1.69 -     1.81: 24
  Bond restraints: 13166
  Sorted by residual:
  bond pdb=" C   SER D  32 "
       pdb=" N   ARG D  33 "
    ideal  model  delta    sigma   weight residual
    1.330  1.257  0.073 1.39e-02 5.18e+03 2.73e+01
  bond pdb=" CZ  ARG E 131 "
       pdb=" NH2 ARG E 131 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.22e+01
  bond pdb=" CZ  ARG G  88 "
       pdb=" NH2 ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG E 116 "
       pdb=" NH2 ARG E 116 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.45e+00
  bond pdb=" CZ  ARG D  72 "
       pdb=" NH2 ARG D  72 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.27e+00
  ... (remaining 13161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 18407
        2.25 -     4.50: 671
        4.50 -     6.75: 33
        6.75 -     9.00: 0
        9.00 -    11.25: 1
  Bond angle restraints: 19112
  Sorted by residual:
  angle pdb=" C   SER D  32 "
        pdb=" CA  SER D  32 "
        pdb=" CB  SER D  32 "
      ideal   model   delta    sigma   weight residual
     110.42  121.67  -11.25 1.99e+00 2.53e-01 3.20e+01
  angle pdb=" O   SER D  32 "
        pdb=" C   SER D  32 "
        pdb=" N   ARG D  33 "
      ideal   model   delta    sigma   weight residual
     122.59  116.13    6.46 1.33e+00 5.65e-01 2.36e+01
  angle pdb=" CA  PRO A  38 "
        pdb=" N   PRO A  38 "
        pdb=" CD  PRO A  38 "
      ideal   model   delta    sigma   weight residual
     112.00  106.41    5.59 1.40e+00 5.10e-01 1.60e+01
  angle pdb=" CA  ILE H  61 "
        pdb=" CB  ILE H  61 "
        pdb=" CG1 ILE H  61 "
      ideal   model   delta    sigma   weight residual
     110.40  117.02   -6.62 1.70e+00 3.46e-01 1.52e+01
  angle pdb=" CD  ARG E 131 "
        pdb=" NE  ARG E 131 "
        pdb=" CZ  ARG E 131 "
      ideal   model   delta    sigma   weight residual
     124.40  129.82   -5.42 1.40e+00 5.10e-01 1.50e+01
  ... (remaining 19107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.16: 5357
       32.16 -    64.31: 1688
       64.31 -    96.47: 53
       96.47 -   128.63: 0
      128.63 -   160.79: 2
  Dihedral angle restraints: 7100
    sinusoidal: 4927
      harmonic: 2173
  Sorted by residual:
  dihedral pdb=" C   SER D  32 "
           pdb=" N   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.37   17.77     0      2.50e+00 1.60e-01 5.05e+01
  dihedral pdb=" N   SER D  32 "
           pdb=" C   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.82  -13.02     0      2.50e+00 1.60e-01 2.71e+01
  dihedral pdb=" CA  ARG D  33 "
           pdb=" C   ARG D  33 "
           pdb=" N   LYS D  34 "
           pdb=" CA  LYS D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 7097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 2123
       0.119 -    0.238: 41
       0.238 -    0.357: 6
       0.357 -    0.476: 0
       0.476 -    0.595: 1
  Chirality restraints: 2171
  Sorted by residual:
  chirality pdb=" CA  SER D  32 "
            pdb=" N   SER D  32 "
            pdb=" C   SER D  32 "
            pdb=" CB  SER D  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.60 2.00e-01 2.50e+01 8.86e+00
  chirality pdb=" CA  PRO B  32 "
            pdb=" N   PRO B  32 "
            pdb=" C   PRO B  32 "
            pdb=" CB  PRO B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO F  32 "
            pdb=" N   PRO F  32 "
            pdb=" C   PRO F  32 "
            pdb=" CB  PRO F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 2168 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  40 "   -0.099 2.00e-02 2.50e+03   5.09e-02 5.18e+01
        pdb=" CG  TYR D  40 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  40 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  40 "    0.057 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  40 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  40 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR D  40 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  17 "   -0.531 9.50e-02 1.11e+02   2.38e-01 3.48e+01
        pdb=" NE  ARG G  17 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  17 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  17 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  17 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -76 "    0.052 2.00e-02 2.50e+03   2.80e-02 1.96e+01
        pdb=" N1   DT I -76 "   -0.070 2.00e-02 2.50e+03
        pdb=" C2   DT I -76 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT I -76 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I -76 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DT I -76 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I -76 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DT I -76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I -76 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I -76 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 8
        2.47 -     3.08: 7511
        3.08 -     3.69: 20503
        3.69 -     4.29: 32533
        4.29 -     4.90: 46271
  Nonbonded interactions: 106826
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F  68 "
            pdb=" NH1 ARG F  92 "
     model   vdw
     1.865 3.120
  nonbonded pdb=" NH2 ARG F  92 "
            pdb=" O   LEU H 100 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH1 ARG H  92 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" O   ASN D  67 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.403 3.040
  ... (remaining 106821 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77))
  selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.900
  Find NCS groups from input model:        0.160
  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:9.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
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      :  0.005   0.111  13166  Z= 0.308
  Angle     :  0.857  11.254  19112  Z= 0.565
  Chirality :  0.048   0.595   2171
  Planarity :  0.012   0.238   1347
  Dihedral  : 28.861 160.785   5702
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.14 %
  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 aren not related in a simple way.
  whole:  0.24 (0.27), residues: 737
  helix:  0.48 (0.20), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.40 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  63 
 TYR   0.099   0.004   TYR D  40 
 PHE   0.012   0.002   PHE A  84 
 HIS   0.006   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (13166)
  covalent geometry    : angle       0.85675 (19112)
  hydrogen bonds       : bond        0.10462 (  810)
  hydrogen bonds       : angle       4.26159 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7253 (mt) cc_final: 0.7029 (mt)
REVERT: A  106 ASP cc_start: 0.6034 (m-30) cc_final: 0.5524 (m-30)
REVERT: A  120 MET cc_start: 0.6701 (mtt) cc_final: 0.6388 (mtm)
REVERT: A  123 ASP cc_start: 0.6922 (m-30) cc_final: 0.6526 (m-30)
REVERT: A  128 ARG cc_start: 0.6531 (mtp180) cc_final: 0.6273 (mmm160)
REVERT: B   79 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6554 (mmtp)
REVERT: B   84 MET cc_start: 0.6224 (mmm) cc_final: 0.5991 (mmp)
REVERT: C  104 GLN cc_start: 0.7350 (tp40) cc_final: 0.6913 (mp10)
REVERT: E   53 ARG cc_start: 0.6337 (ttp-110) cc_final: 0.5974 (ttp-110)
REVERT: E  120 MET cc_start: 0.6824 (mtt) cc_final: 0.6491 (mtm)
REVERT: E  122 LYS cc_start: 0.6425 (pttt) cc_final: 0.6153 (pttp)
REVERT: G   40 SER cc_start: 0.7793 (p) cc_final: 0.7524 (p)
REVERT: G   42 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5392 (mtp85)
REVERT: G   89 ASN cc_start: 0.7383 (m-40) cc_final: 0.6977 (m110)
REVERT: H   71 GLU cc_start: 0.6421 (pt0) cc_final: 0.6035 (pt0)
REVERT: H  108 LYS cc_start: 0.7308 (tttp) cc_final: 0.7021 (ttpp)
  outliers start: 0
  outliers final: 1
  residues processed: 146
  average time/residue: 0.9834
  time to fit residues: 150.7557
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
F  25 ASN
F  27 GLN
F  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.118325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.102719 restraints weight = 16197.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 0.82
r_work: 0.3189 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13166  Z= 0.175
  Angle     :  0.555   5.014  19112  Z= 0.346
  Chirality :  0.035   0.135   2171
  Planarity :  0.004   0.035   1347
  Dihedral  : 30.300 170.433   4225
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.50 %
    Favored  : 81.38 %
  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 aren not related in a simple way.
  whole:  2.95 (0.30), residues: 737
  helix:  2.68 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.012   0.001   TYR H  40 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (13166)
  covalent geometry    : angle       0.55506 (19112)
  hydrogen bonds       : bond        0.04450 (  810)
  hydrogen bonds       : angle       2.79060 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.8009 (mtt-85)
REVERT: A   83 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6433 (mtm180)
REVERT: A  106 ASP cc_start: 0.7558 (m-30) cc_final: 0.7353 (m-30)
REVERT: C  104 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7590 (mp10)
REVERT: D   71 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7355 (mt-10)
REVERT: E  120 MET cc_start: 0.7898 (mtt) cc_final: 0.7695 (mtm)
REVERT: F   78 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8489 (mtm-85)
REVERT: G   73 ASN cc_start: 0.7857 (t0) cc_final: 0.7572 (t160)
REVERT: G   89 ASN cc_start: 0.8583 (m-40) cc_final: 0.8327 (m110)
REVERT: H   79 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7741 (mtt90)
REVERT: H   85 LYS cc_start: 0.8529 (mttp) cc_final: 0.8303 (mttp)
  outliers start: 7
  outliers final: 0
  residues processed: 126
  average time/residue: 0.9307
  time to fit residues: 123.4227
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
B  93 GLN
C  73 ASN
E  68 GLN
F  25 ASN
F  75 HIS
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.111192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.095240 restraints weight = 16106.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 0.84
r_work: 0.3065 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  13166  Z= 0.291
  Angle     :  0.633   5.922  19112  Z= 0.387
  Chirality :  0.042   0.143   2171
  Planarity :  0.005   0.043   1347
  Dihedral  : 30.311 173.117   4223
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.58 %
    Favored  : 78.01 %
  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 aren not related in a simple way.
  whole:  2.71 (0.30), residues: 737
  helix:  2.51 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.32 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  71 
 TYR   0.017   0.002   TYR D  40 
 PHE   0.009   0.002   PHE H  70 
 HIS   0.007   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 (13166)
  covalent geometry    : angle       0.63308 (19112)
  hydrogen bonds       : bond        0.05952 (  810)
  hydrogen bonds       : angle       2.92088 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7683 (mtt90)
REVERT: A   63 ARG cc_start: 0.8461 (mmp80) cc_final: 0.7954 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.6824 (mtm180)
REVERT: A  128 ARG cc_start: 0.8643 (mtp180) cc_final: 0.8262 (mmm160)
REVERT: D   62 MET cc_start: 0.8593 (mmp) cc_final: 0.8369 (mmt)
REVERT: D   71 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7174 (mp0)
REVERT: G   73 ASN cc_start: 0.8170 (t0) cc_final: 0.7879 (t160)
REVERT: G   89 ASN cc_start: 0.8766 (m-40) cc_final: 0.8552 (m-40)
REVERT: G   91 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.4885 (tp30)
  outliers start: 15
  outliers final: 5
  residues processed: 103
  average time/residue: 1.0229
  time to fit residues: 110.3448
Evaluate side-chains
  103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.113577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097824 restraints weight = 16029.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 0.82
r_work: 0.3091 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.170
  Angle     :  0.584   6.535  19112  Z= 0.365
  Chirality :  0.037   0.124   2171
  Planarity :  0.005   0.094   1347
  Dihedral  : 30.338 173.524   4223
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.06 %
    Favored  : 77.85 %
  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 aren not related in a simple way.
  whole:  2.91 (0.30), residues: 737
  helix:  2.67 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.29 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  36 
 TYR   0.018   0.001   TYR F  88 
 PHE   0.016   0.001   PHE D  70 
 HIS   0.002   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13166)
  covalent geometry    : angle       0.58393 (19112)
  hydrogen bonds       : bond        0.04764 (  810)
  hydrogen bonds       : angle       2.83580 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7589 (mtt90)
REVERT: A   63 ARG cc_start: 0.8383 (mmp80) cc_final: 0.7987 (mmt-90)
REVERT: A  128 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8220 (mmm160)
REVERT: C   91 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.3128 (tp30)
REVERT: C  104 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7778 (mp10)
REVERT: D   62 MET cc_start: 0.8565 (mmp) cc_final: 0.8287 (mmt)
REVERT: D   71 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7081 (mp0)
REVERT: G   73 ASN cc_start: 0.8138 (t0) cc_final: 0.7832 (t160)
REVERT: G   91 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.4754 (tp30)
  outliers start: 13
  outliers final: 4
  residues processed: 99
  average time/residue: 1.1506
  time to fit residues: 118.5490
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097978 restraints weight = 16124.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 0.83
r_work: 0.3094 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13166  Z= 0.211
  Angle     :  0.572   5.052  19112  Z= 0.355
  Chirality :  0.037   0.126   2171
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.243 172.498   4223
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.74 %
    Favored  : 78.17 %
  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 aren not related in a simple way.
  whole:  2.96 (0.30), residues: 737
  helix:  2.71 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.27 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  71 
 TYR   0.014   0.002   TYR F  88 
 PHE   0.006   0.001   PHE D  70 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (13166)
  covalent geometry    : angle       0.57203 (19112)
  hydrogen bonds       : bond        0.04684 (  810)
  hydrogen bonds       : angle       2.75080 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7595 (mtt90)
REVERT: A  128 ARG cc_start: 0.8631 (mtp180) cc_final: 0.8259 (mmm160)
REVERT: B   95 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7455 (mtp-110)
REVERT: C  104 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7757 (mp10)
REVERT: D   62 MET cc_start: 0.8591 (mmp) cc_final: 0.8329 (mmt)
REVERT: D   71 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7075 (mp0)
REVERT: G   73 ASN cc_start: 0.8185 (t0) cc_final: 0.7768 (t0)
REVERT: G   77 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8155 (mtm180)
REVERT: G   91 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.4813 (tp30)
REVERT: H   93 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7120 (mp0)
  outliers start: 13
  outliers final: 4
  residues processed: 95
  average time/residue: 1.0029
  time to fit residues: 99.4381
Evaluate side-chains
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.114185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.098290 restraints weight = 15993.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 0.82
r_work: 0.3101 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.189
  Angle     :  0.571   5.208  19112  Z= 0.354
  Chirality :  0.036   0.124   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.252 172.529   4223
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.71 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.02 (0.30), residues: 737
  helix:  2.77 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.27 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  71 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.005   0.001   PHE A  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13166)
  covalent geometry    : angle       0.57117 (19112)
  hydrogen bonds       : bond        0.04563 (  810)
  hydrogen bonds       : angle       2.73755 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7565 (mtt90)
REVERT: A  128 ARG cc_start: 0.8634 (mtp180) cc_final: 0.8260 (mmm160)
REVERT: B   95 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7485 (mtt-85)
REVERT: C  104 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7759 (mp10)
REVERT: D   62 MET cc_start: 0.8584 (mmp) cc_final: 0.8308 (mmt)
REVERT: D   71 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7072 (mp0)
REVERT: G   73 ASN cc_start: 0.8182 (t0) cc_final: 0.7877 (t160)
REVERT: G   91 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.4797 (tp30)
REVERT: H   93 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7104 (mp0)
  outliers start: 10
  outliers final: 4
  residues processed: 92
  average time/residue: 1.0776
  time to fit residues: 103.6212
Evaluate side-chains
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.098224 restraints weight = 15884.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 0.82
r_work: 0.3116 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.193
  Angle     :  0.566   5.053  19112  Z= 0.351
  Chirality :  0.036   0.124   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.243 172.741   4223
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.55 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.02 (0.30), residues: 737
  helix:  2.77 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.27 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.005   0.001   PHE A  67 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (13166)
  covalent geometry    : angle       0.56562 (19112)
  hydrogen bonds       : bond        0.04563 (  810)
  hydrogen bonds       : angle       2.71898 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7580 (mtt90)
REVERT: A  128 ARG cc_start: 0.8643 (mtp180) cc_final: 0.8281 (mmm160)
REVERT: B   95 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7437 (mtp-110)
REVERT: C  104 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7757 (mp10)
REVERT: D   62 MET cc_start: 0.8580 (mmp) cc_final: 0.8296 (mmt)
REVERT: D   71 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7157 (mp0)
REVERT: G   73 ASN cc_start: 0.8198 (t0) cc_final: 0.7881 (t160)
REVERT: G   91 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.4813 (tp30)
REVERT: H   93 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7123 (mp0)
  outliers start: 11
  outliers final: 4
  residues processed: 94
  average time/residue: 1.1586
  time to fit residues: 113.6884
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 27 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.098501 restraints weight = 15985.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 0.82
r_work: 0.3120 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.185
  Angle     :  0.567  10.063  19112  Z= 0.351
  Chirality :  0.036   0.124   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.244 172.737   4223
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.06 %
    Favored  : 77.37 %
  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 aren not related in a simple way.
  whole:  3.07 (0.30), residues: 737
  helix:  2.80 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.26 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.005   0.001   PHE A  67 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (13166)
  covalent geometry    : angle       0.56738 (19112)
  hydrogen bonds       : bond        0.04493 (  810)
  hydrogen bonds       : angle       2.71315 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7577 (mtt90)
REVERT: A  128 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8280 (mmm160)
REVERT: B   95 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7386 (mtp-110)
REVERT: C   64 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7928 (tt0)
REVERT: C  104 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7756 (mp10)
REVERT: D   62 MET cc_start: 0.8579 (mmp) cc_final: 0.8290 (mmt)
REVERT: D   71 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7153 (mp0)
REVERT: G   73 ASN cc_start: 0.8165 (t0) cc_final: 0.7856 (t160)
REVERT: G   91 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.4814 (tp30)
REVERT: H   93 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7118 (mp0)
  outliers start: 16
  outliers final: 5
  residues processed: 98
  average time/residue: 1.1156
  time to fit residues: 114.1997
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.114493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.098569 restraints weight = 15953.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 0.82
r_work: 0.3105 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.184
  Angle     :  0.561   5.681  19112  Z= 0.349
  Chirality :  0.036   0.124   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.237 172.868   4223
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.39 %
    Favored  : 77.37 %
  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 aren not related in a simple way.
  whole:  3.07 (0.30), residues: 737
  helix:  2.80 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.25 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.020   0.001   TYR F  88 
 PHE   0.005   0.001   PHE A  67 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (13166)
  covalent geometry    : angle       0.56078 (19112)
  hydrogen bonds       : bond        0.04465 (  810)
  hydrogen bonds       : angle       2.69982 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7582 (mtt90)
REVERT: A  128 ARG cc_start: 0.8633 (mtp180) cc_final: 0.8268 (mmm160)
REVERT: B   95 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7439 (mtp-110)
REVERT: C   64 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7936 (tt0)
REVERT: C  104 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7761 (mp10)
REVERT: D   62 MET cc_start: 0.8575 (mmp) cc_final: 0.8285 (mmt)
REVERT: D   71 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7139 (mp0)
REVERT: G   73 ASN cc_start: 0.8143 (t0) cc_final: 0.7830 (t160)
REVERT: G   91 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.4802 (tp30)
REVERT: H   79 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7862 (mtt90)
REVERT: H   93 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7073 (mp0)
  outliers start: 14
  outliers final: 5
  residues processed: 97
  average time/residue: 1.2852
  time to fit residues: 130.0857
Evaluate side-chains
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0060
   chunk 84 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.098971 restraints weight = 16077.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 0.82
r_work: 0.3112 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.166
  Angle     :  0.558   5.971  19112  Z= 0.347
  Chirality :  0.035   0.125   2171
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.238 172.810   4223
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.55 %
    Favored  : 77.37 %
  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 aren not related in a simple way.
  whole:  3.12 (0.30), residues: 737
  helix:  2.83 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (13166)
  covalent geometry    : angle       0.55781 (19112)
  hydrogen bonds       : bond        0.04367 (  810)
  hydrogen bonds       : angle       2.69910 ( 2008)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7552 (mtt90)
REVERT: A  128 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8275 (mmm160)
REVERT: B   95 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7396 (mtp-110)
REVERT: C   64 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7942 (tt0)
REVERT: C  104 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7754 (mp10)
REVERT: D   62 MET cc_start: 0.8568 (mmp) cc_final: 0.8276 (mmt)
REVERT: D   71 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: G   73 ASN cc_start: 0.8137 (t0) cc_final: 0.7825 (t160)
REVERT: G   91 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.4795 (tp30)
REVERT: H   79 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7858 (mtt90)
REVERT: H   93 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7076 (mp0)
  outliers start: 13
  outliers final: 5
  residues processed: 96
  average time/residue: 1.3148
  time to fit residues: 131.5562
Evaluate side-chains
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.0020
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.114371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.099104 restraints weight = 16239.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 0.78
r_work: 0.3141 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.167
  Angle     :  0.552   5.431  19112  Z= 0.345
  Chirality :  0.035   0.124   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.229 173.061   4223
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.71 %
    Favored  : 77.21 %
  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 aren not related in a simple way.
  whole:  3.15 (0.30), residues: 737
  helix:  2.85 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  71 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.002   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13166)
  covalent geometry    : angle       0.55228 (19112)
  hydrogen bonds       : bond        0.04286 (  810)
  hydrogen bonds       : angle       2.67436 ( 2008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3937.96 seconds
wall clock time: 67 minutes 38.27 seconds (4058.27 seconds total)