Starting phenix.real_space_refine
on Fri Jul  3 17:20:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pfd_13372/07_2026/7pfd_13372.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     344      5.49       5
     S      10      5.16       5
     C    7520      2.51       5
     N    2563      2.21       5
     O    3238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 13675
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3541
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "I"
      Number of atoms: 3511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3511
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "U"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.97, per 1000 atoms: 0.22
  Number of scatterers: 13675
  At special positions: 0
  Unit cell: (111.3, 160.65, 114.45, 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     344     15.00
     O    3238      8.00
     N    2563      7.00
     C    7520      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: 1.09
  Conformation dependent library (CDL) restraints added in 385.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      68.8% alpha, 2.8% beta
      169 base pairs and 294 stacking pairs defined.
    Time for finding SS restraints: 2.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.842A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.537A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.533A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.507A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.564A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.796A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.544A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.641A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    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: 4.313A  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 'H' and resid 37 through 49
      removed outlier: 3.573A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
    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 helix  chain 'U' and resid 38 through 49
      removed outlier: 3.967A  pdb=" N   LEU U  42 " --> pdb=" O   PRO U  38 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 57 through 69
    Processing helix  chain 'U' and resid 75 through 90
      removed outlier: 3.971A  pdb=" N   LYS U  84 " --> pdb=" O   LYS U  80 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL U  87 " --> pdb=" O   LEU U  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.283A  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 97
      removed outlier: 6.192A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.846A  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
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.967A  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: 7.503A  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 'U' and resid 92 through 94

    429 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      431 hydrogen bonds
      862 hydrogen bond angles
      0 basepair planarities
      169 basepair parallelities
      294 stacking parallelities
  Total time for adding SS restraints: 3.16

  Time building geometry restraints manager: 1.47 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: 2420
        1.33 -     1.45: 5050
        1.45 -     1.57: 6440
        1.57 -     1.69: 686
        1.69 -     1.82: 20
  Bond restraints: 14616
  Sorted by residual:
  bond pdb=" C3'  DG J 763 "
       pdb=" O3'  DG J 763 "
    ideal  model  delta    sigma   weight residual
    1.435  1.497 -0.062 1.30e-02 5.92e+03 2.27e+01
  bond pdb=" C5'  DA I 182 "
       pdb=" C4'  DA I 182 "
    ideal  model  delta    sigma   weight residual
    1.512  1.544 -0.032 7.00e-03 2.04e+04 2.04e+01
  bond pdb=" C3'  DC I 168 "
       pdb=" O3'  DC I 168 "
    ideal  model  delta    sigma   weight residual
    1.435  1.380  0.055 1.30e-02 5.92e+03 1.80e+01
  bond pdb=" C3'  DC I 136 "
       pdb=" O3'  DC I 136 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.36e+01
  bond pdb=" C5'  DA I  84 "
       pdb=" C4'  DA I  84 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.35e+01
  ... (remaining 14611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 20851
        2.99 -     5.98: 322
        5.98 -     8.97: 30
        8.97 -    11.96: 2
       11.96 -    14.95: 3
  Bond angle restraints: 21208
  Sorted by residual:
  angle pdb=" O4'  DA I 166 "
        pdb=" C4'  DA I 166 "
        pdb=" C3'  DA I 166 "
      ideal   model   delta    sigma   weight residual
     106.00  101.66    4.34 6.00e-01 2.78e+00 5.24e+01
  angle pdb=" O4'  DG I 127 "
        pdb=" C4'  DG I 127 "
        pdb=" C3'  DG I 127 "
      ideal   model   delta    sigma   weight residual
     106.00  102.41    3.59 6.00e-01 2.78e+00 3.59e+01
  angle pdb=" O4'  DC J 688 "
        pdb=" C1'  DC J 688 "
        pdb=" N1   DC J 688 "
      ideal   model   delta    sigma   weight residual
     108.00  112.17   -4.17 7.00e-01 2.04e+00 3.55e+01
  angle pdb=" N   GLU H 113 "
        pdb=" CA  GLU H 113 "
        pdb=" CB  GLU H 113 "
      ideal   model   delta    sigma   weight residual
     110.28  119.29   -9.01 1.55e+00 4.16e-01 3.38e+01
  angle pdb=" O4'  DA I  45 "
        pdb=" C4'  DA I  45 "
        pdb=" C3'  DA I  45 "
      ideal   model   delta    sigma   weight residual
     106.00  102.53    3.47 6.00e-01 2.78e+00 3.35e+01
  ... (remaining 21203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.86: 6098
       35.86 -    71.73: 1769
       71.73 -   107.59: 49
      107.59 -   143.46: 1
      143.46 -   179.32: 2
  Dihedral angle restraints: 7919
    sinusoidal: 5488
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  LEU B  22 "
           pdb=" C   LEU B  22 "
           pdb=" N   ARG B  23 "
           pdb=" CA  ARG B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.60  -20.40     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" C4'  DG I 119 "
           pdb=" C3'  DG I 119 "
           pdb=" O3'  DG I 119 "
           pdb=" P    DC I 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.68  179.32     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   GLN A  85 "
           pdb=" CA  GLN A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.32   19.68     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 7916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1611
       0.047 -    0.094: 636
       0.094 -    0.142: 136
       0.142 -    0.189: 24
       0.189 -    0.236: 9
  Chirality restraints: 2416
  Sorted by residual:
  chirality pdb=" CB  THR G  59 "
            pdb=" CA  THR G  59 "
            pdb=" OG1 THR G  59 "
            pdb=" CG2 THR G  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  PHE E 104 "
            pdb=" N   PHE E 104 "
            pdb=" C   PHE E 104 "
            pdb=" CB  PHE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 2413 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.052 5.00e-02 4.00e+02   7.88e-02 9.94e+00
        pdb=" N   PRO G  80 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H 113 "    0.015 2.00e-02 2.50e+03   3.14e-02 9.87e+00
        pdb=" CD  GLU H 113 "   -0.054 2.00e-02 2.50e+03
        pdb=" OE1 GLU H 113 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU H 113 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  70 "   -0.015 2.00e-02 2.50e+03   2.91e-02 8.49e+00
        pdb=" C   VAL F  70 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL F  70 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR F  71 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 2628
        2.78 -     3.31: 12748
        3.31 -     3.84: 30087
        3.84 -     4.37: 33559
        4.37 -     4.90: 45685
  Nonbonded interactions: 124707
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 118 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   LYS G  15 "
            pdb=" NH1 ARG G  20 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NH1 ARG C  81 "
            pdb=" O   VAL C 107 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH2 ARG D  33 "
            pdb=" O2   DC I  51 "
     model   vdw
     2.296 3.120
  ... (remaining 124702 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.030
  Process input model:                     15.160
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
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   0.062  14616  Z= 0.616
  Angle     :  1.040  14.946  21208  Z= 0.838
  Chirality :  0.052   0.236   2416
  Planarity :  0.007   0.079   1488
  Dihedral  : 29.935 179.324   6353
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.57 (0.26), residues: 825
  helix:  0.04 (0.20), residues: 560
  sheet: -3.84 (0.84), residues: 10
  loop : -0.91 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  67 
 TYR   0.023   0.003   TYR G  50 
 PHE   0.020   0.003   PHE C  25 
 HIS   0.010   0.003   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00687 /  0.62 (14616)
  covalent geometry    : angle       1.03973 /  0.84 (21208)
  hydrogen bonds       : bond        0.11370 /  7.79 (  860)
  hydrogen bonds       : angle       4.75167 /  3.44 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8488 (t80) cc_final: 0.8221 (t80)
REVERT: A  104 PHE cc_start: 0.9578 (m-10) cc_final: 0.9329 (m-80)
REVERT: E  105 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8961 (mm-30)
REVERT: G   34 LEU cc_start: 0.8427 (mt) cc_final: 0.8216 (mt)
REVERT: H   98 VAL cc_start: 0.9711 (t) cc_final: 0.9467 (p)
REVERT: H  102 LEU cc_start: 0.8816 (mp) cc_final: 0.8425 (tp)
REVERT: H  106 LEU cc_start: 0.9767 (mt) cc_final: 0.9410 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1077
  time to fit residues: 17.2817
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
E  93 GLN
E 108 ASN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.039863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.032031 restraints weight = 195703.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.033072 restraints weight = 114888.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.033788 restraints weight = 80932.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.034276 restraints weight = 62428.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.034680 restraints weight = 51938.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14616  Z= 0.204
  Angle     :  0.760   9.234  21208  Z= 0.445
  Chirality :  0.050   0.289   2416
  Planarity :  0.005   0.069   1488
  Dihedral  : 33.659 174.143   4701
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.17 %
    Favored  : 96.39 %
  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:  0.22 (0.27), residues: 825
  helix:  0.68 (0.21), residues: 578
  sheet: -4.15 (0.84), residues: 10
  loop : -0.77 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  86 
 TYR   0.017   0.002   TYR E  99 
 PHE   0.012   0.002   PHE B 100 
 HIS   0.006   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.20 (14616)
  covalent geometry    : angle       0.75975 /  0.45 (21208)
  hydrogen bonds       : bond        0.08453 /  5.77 (  860)
  hydrogen bonds       : angle       3.75809 /  2.74 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8069 (t80) cc_final: 0.7830 (t80)
REVERT: E  105 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8780 (mm-30)
REVERT: F   97 LEU cc_start: 0.7648 (tp) cc_final: 0.7381 (tp)
REVERT: H   98 VAL cc_start: 0.9439 (t) cc_final: 0.9191 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0937
  time to fit residues: 13.8162
Evaluate side-chains
  67 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 93 optimal weight:   30.0000
   chunk 86 optimal weight:   30.0000
   chunk 10 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
G 112 GLN
H  47 GLN
H 109 HIS
U  75 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.037032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.029903 restraints weight = 189198.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.030946 restraints weight = 104467.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.031689 restraints weight = 70243.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.032232 restraints weight = 52326.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.032609 restraints weight = 41815.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14616  Z= 0.219
  Angle     :  0.760   8.582  21208  Z= 0.443
  Chirality :  0.049   0.297   2416
  Planarity :  0.006   0.068   1488
  Dihedral  : 33.813 178.514   4701
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  4.33 %
    Favored  : 94.66 %
  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:  0.13 (0.27), residues: 825
  helix:  0.61 (0.20), residues: 588
  sheet: -3.69 (1.09), residues: 10
  loop : -0.91 (0.36), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  79 
 TYR   0.041   0.003   TYR D  42 
 PHE   0.014   0.002   PHE B 100 
 HIS   0.005   0.002   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.22 (14616)
  covalent geometry    : angle       0.76046 /  0.44 (21208)
  hydrogen bonds       : bond        0.10052 /  6.80 (  860)
  hydrogen bonds       : angle       3.69314 /  2.67 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 LEU cc_start: 0.6670 (tp) cc_final: 0.6446 (tp)
REVERT: E  105 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8739 (mm-30)
  outliers start: 7
  outliers final: 3
  residues processed: 99
  average time/residue: 0.1093
  time to fit residues: 16.3790
Evaluate side-chains
  66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:   30.0000
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 103 optimal weight:   30.0000
   chunk 44 optimal weight:    0.0970
   chunk 86 optimal weight:   30.0000
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 87 optimal weight:   30.0000
   overall best weight:    2.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
G 112 GLN
H  47 GLN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.038818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.031103 restraints weight = 196019.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.032115 restraints weight = 116372.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.032791 restraints weight = 81987.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.033304 restraints weight = 63782.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.033669 restraints weight = 52801.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14616  Z= 0.167
  Angle     :  0.712   8.585  21208  Z= 0.415
  Chirality :  0.048   0.306   2416
  Planarity :  0.005   0.080   1488
  Dihedral  : 33.766 176.459   4701
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  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:  0.43 (0.28), residues: 825
  helix:  0.85 (0.21), residues: 586
  sheet: -3.45 (1.25), residues: 10
  loop : -0.83 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  33 
 TYR   0.031   0.002   TYR D  40 
 PHE   0.025   0.002   PHE E 104 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.17 (14616)
  covalent geometry    : angle       0.71151 /  0.42 (21208)
  hydrogen bonds       : bond        0.06800 /  4.64 (  860)
  hydrogen bonds       : angle       3.67529 /  2.67 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.8895 (m-80) cc_final: 0.8399 (m-80)
REVERT: E  104 PHE cc_start: 0.9080 (m-80) cc_final: 0.8877 (m-80)
REVERT: E  105 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8743 (mm-30)
REVERT: F   97 LEU cc_start: 0.7930 (tp) cc_final: 0.7678 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1051
  time to fit residues: 14.9640
Evaluate side-chains
  69 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 79 optimal weight:   30.0000
   chunk 84 optimal weight:   30.0000
   chunk 54 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    3.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
G  84 GLN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.038335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.032292 restraints weight = 213278.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.033128 restraints weight = 131656.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.033664 restraints weight = 93420.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.034091 restraints weight = 73575.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.034428 restraints weight = 60470.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14616  Z= 0.180
  Angle     :  0.717   8.203  21208  Z= 0.417
  Chirality :  0.047   0.301   2416
  Planarity :  0.005   0.081   1488
  Dihedral  : 33.674 176.996   4701
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.55 (0.28), residues: 825
  helix:  0.96 (0.21), residues: 580
  sheet: -2.77 (1.66), residues: 10
  loop : -0.85 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.019   0.002   TYR H  42 
 PHE   0.032   0.002   PHE A 104 
 HIS   0.005   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.18 (14616)
  covalent geometry    : angle       0.71689 /  0.42 (21208)
  hydrogen bonds       : bond        0.07833 /  5.33 (  860)
  hydrogen bonds       : angle       3.68052 /  2.67 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ILE cc_start: 0.9787 (tp) cc_final: 0.9582 (pt)
REVERT: B   68 ASP cc_start: 0.9560 (m-30) cc_final: 0.9330 (m-30)
REVERT: E  104 PHE cc_start: 0.9619 (m-80) cc_final: 0.9354 (m-80)
REVERT: E  105 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8860 (mm-30)
REVERT: F   53 GLU cc_start: 0.9638 (tp30) cc_final: 0.9424 (tm-30)
REVERT: G   73 ASN cc_start: 0.8926 (t0) cc_final: 0.8719 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1140
  time to fit residues: 15.4115
Evaluate side-chains
  69 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 46 optimal weight:    5.9990
   chunk 102 optimal weight:   30.0000
   chunk 108 optimal weight:   30.0000
   chunk 73 optimal weight:   30.0000
   chunk 18 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 95 optimal weight:   40.0000
   overall best weight:    5.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
G 112 GLN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.034707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.027885 restraints weight = 214555.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.028781 restraints weight = 124807.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.029409 restraints weight = 87451.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.029827 restraints weight = 67769.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.030168 restraints weight = 56544.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14616  Z= 0.238
  Angle     :  0.770   8.960  21208  Z= 0.443
  Chirality :  0.049   0.299   2416
  Planarity :  0.006   0.055   1488
  Dihedral  : 33.883 176.223   4701
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 22.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.46 %
    Favored  : 96.10 %
  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: -0.01 (0.27), residues: 825
  helix:  0.56 (0.20), residues: 586
  sheet: -2.56 (1.79), residues: 10
  loop : -1.20 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  42 
 TYR   0.020   0.003   TYR D  40 
 PHE   0.020   0.002   PHE E  78 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.24 (14616)
  covalent geometry    : angle       0.77006 /  0.44 (21208)
  hydrogen bonds       : bond        0.11548 /  7.83 (  860)
  hydrogen bonds       : angle       3.87501 /  2.81 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 LEU cc_start: 0.7848 (tp) cc_final: 0.7450 (tp)
REVERT: F   53 GLU cc_start: 0.9146 (tp30) cc_final: 0.8912 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 87
  average time/residue: 0.1059
  time to fit residues: 14.3175
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:   30.0000
   chunk 21 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0030
   overall best weight:    2.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
H  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.035748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.028676 restraints weight = 205129.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.029651 restraints weight = 119857.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.030325 restraints weight = 83352.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.030779 restraints weight = 63773.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.031111 restraints weight = 52502.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14616  Z= 0.172
  Angle     :  0.731   9.656  21208  Z= 0.421
  Chirality :  0.048   0.307   2416
  Planarity :  0.005   0.059   1488
  Dihedral  : 33.870 174.809   4701
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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:  0.24 (0.28), residues: 825
  helix:  0.73 (0.21), residues: 582
  sheet: -2.39 (1.89), residues: 10
  loop : -1.01 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E  83 
 TYR   0.020   0.002   TYR D  40 
 PHE   0.029   0.002   PHE A 104 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.17 (14616)
  covalent geometry    : angle       0.73053 /  0.42 (21208)
  hydrogen bonds       : bond        0.06930 /  4.74 (  860)
  hydrogen bonds       : angle       3.89355 /  2.83 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 LEU cc_start: 0.7512 (tp) cc_final: 0.7201 (tp)
REVERT: F   53 GLU cc_start: 0.9115 (tp30) cc_final: 0.8902 (tm-30)
REVERT: F   97 LEU cc_start: 0.8327 (tp) cc_final: 0.8108 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1206
  time to fit residues: 15.8749
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 100 optimal weight:   30.0000
   chunk 55 optimal weight:    0.4980
   chunk 25 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   chunk 85 optimal weight:   30.0000
   chunk 109 optimal weight:    0.1980
   chunk 112 optimal weight:   30.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
H  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.035659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.028564 restraints weight = 207389.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.029492 restraints weight = 121588.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.030132 restraints weight = 85569.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.030607 restraints weight = 66140.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.030938 restraints weight = 54362.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14616  Z= 0.176
  Angle     :  0.717   7.875  21208  Z= 0.414
  Chirality :  0.047   0.297   2416
  Planarity :  0.005   0.058   1488
  Dihedral  : 33.704 176.744   4701
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  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:  0.38 (0.28), residues: 825
  helix:  0.85 (0.21), residues: 582
  sheet: -2.55 (1.90), residues: 10
  loop : -1.00 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  32 
 TYR   0.025   0.002   TYR F  98 
 PHE   0.022   0.002   PHE D  65 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.18 (14616)
  covalent geometry    : angle       0.71713 /  0.41 (21208)
  hydrogen bonds       : bond        0.07544 /  5.14 (  860)
  hydrogen bonds       : angle       3.83448 /  2.79 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 LEU cc_start: 0.8579 (tp) cc_final: 0.8224 (mm)
REVERT: E   82 LEU cc_start: 0.7390 (tp) cc_final: 0.7037 (tp)
REVERT: F   53 GLU cc_start: 0.9075 (tp30) cc_final: 0.8849 (tm-30)
REVERT: F   97 LEU cc_start: 0.8132 (tp) cc_final: 0.7800 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1040
  time to fit residues: 13.4916
Evaluate side-chains
  66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 102 optimal weight:   30.0000
   chunk 92 optimal weight:   40.0000
   chunk 83 optimal weight:   40.0000
   chunk 77 optimal weight:   30.0000
   chunk 87 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 79 optimal weight:   30.0000
   overall best weight:   12.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
D  84 ASN
E  76 GLN
E 108 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.031945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.026816 restraints weight = 254769.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.027492 restraints weight = 161028.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.027933 restraints weight = 115278.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.028254 restraints weight = 90710.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.028402 restraints weight = 75948.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.121  14616  Z= 0.465
  Angle     :  1.082  12.951  21208  Z= 0.600
  Chirality :  0.062   0.294   2416
  Planarity :  0.010   0.108   1488
  Dihedral  : 34.408 178.065   4701
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 48.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.25), residues: 825
  helix: -0.68 (0.19), residues: 570
  sheet: -2.66 (1.82), residues: 10
  loop : -1.78 (0.34), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.041   0.002   ARG E  83 
 TYR   0.040   0.005   TYR H  42 
 PHE   0.076   0.006   PHE E 104 
 HIS   0.014   0.003   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00813 /  0.46 (14616)
  covalent geometry    : angle       1.08193 /  0.60 (21208)
  hydrogen bonds       : bond        0.22606 / 15.26 (  860)
  hydrogen bonds       : angle       5.04389 /  3.65 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   78 PHE cc_start: 0.9413 (t80) cc_final: 0.9210 (t80)
REVERT: E  120 MET cc_start: 0.5029 (mtt) cc_final: 0.4786 (mtt)
REVERT: F   53 GLU cc_start: 0.9618 (tp30) cc_final: 0.9367 (tm-30)
REVERT: F   84 MET cc_start: 0.8473 (ppp) cc_final: 0.8255 (ppp)
REVERT: G   72 ASP cc_start: 0.9588 (t70) cc_final: 0.9322 (m-30)
REVERT: H   71 GLU cc_start: 0.9323 (tp30) cc_final: 0.9108 (tp30)
REVERT: H  102 LEU cc_start: 0.8770 (tp) cc_final: 0.8525 (tp)
REVERT: H  105 GLU cc_start: 0.9662 (pm20) cc_final: 0.9432 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0934
  time to fit residues: 10.6280
Evaluate side-chains
  55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 80 optimal weight:   40.0000
   chunk 33 optimal weight:    1.9990
   chunk 99 optimal weight:   30.0000
   chunk 93 optimal weight:   30.0000
   chunk 25 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
E  76 GLN
E 108 ASN
G  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.032277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.025761 restraints weight = 220751.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.026602 restraints weight = 128678.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.027217 restraints weight = 89578.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.027624 restraints weight = 68644.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.027938 restraints weight = 56716.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.4821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14616  Z= 0.240
  Angle     :  0.826  10.779  21208  Z= 0.467
  Chirality :  0.053   0.299   2416
  Planarity :  0.006   0.058   1488
  Dihedral  : 34.541 172.144   4701
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 26.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.26), residues: 825
  helix: -0.01 (0.20), residues: 570
  sheet: -2.80 (1.74), residues: 10
  loop : -1.62 (0.34), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  63 
 TYR   0.030   0.003   TYR D  40 
 PHE   0.024   0.003   PHE B 100 
 HIS   0.011   0.002   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.24 (14616)
  covalent geometry    : angle       0.82594 /  0.47 (21208)
  hydrogen bonds       : bond        0.10858 /  7.40 (  860)
  hydrogen bonds       : angle       4.42550 /  3.20 ( 2146)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   53 GLU cc_start: 0.8945 (tp30) cc_final: 0.8730 (tm-30)
REVERT: F   97 LEU cc_start: 0.8237 (tp) cc_final: 0.8003 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1096
  time to fit residues: 13.4625
Evaluate side-chains
  58 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0870
   chunk 97 optimal weight:   30.0000
   chunk 59 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 87 optimal weight:   40.0000
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    3.0166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
G  38 ASN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.033636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.026887 restraints weight = 212504.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.027786 restraints weight = 124747.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.028424 restraints weight = 86558.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.028889 restraints weight = 66160.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.029203 restraints weight = 53934.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  14616  Z= 0.183
  Angle     :  0.762   8.301  21208  Z= 0.435
  Chirality :  0.050   0.292   2416
  Planarity :  0.005   0.050   1488
  Dihedral  : 34.247 174.617   4701
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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: -0.31 (0.28), residues: 825
  helix:  0.42 (0.21), residues: 588
  sheet: -2.31 (1.93), residues: 10
  loop : -1.58 (0.35), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  77 
 TYR   0.021   0.002   TYR D  40 
 PHE   0.021   0.002   PHE D  65 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.18 (14616)
  covalent geometry    : angle       0.76162 /  0.44 (21208)
  hydrogen bonds       : bond        0.07220 /  4.94 (  860)
  hydrogen bonds       : angle       4.03110 /  2.91 ( 2146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2190.28 seconds
wall clock time: 38 minutes 48.50 seconds (2328.50 seconds total)