Starting phenix.real_space_refine
on Fri May 16 06:19:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8g_29850/05_2025/8g8g_29850.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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     348      5.49       5
     S      17      5.16       5
     C    8089      2.51       5
     N    2711      2.21       5
     O    3393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14558
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 895
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 915
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 3539
          Classifications: {'DNA': 174}
          Link IDs: {'rna3p': 173}
    Chain: "J"
      Number of atoms: 3595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 3595
          Classifications: {'DNA': 174}
          Link IDs: {'rna3p': 173}
    Chain: "X"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1152
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 3, 'TRANS': 136}
          Chain breaks: 1
  Time building chain proxies: 8.15, per 1000 atoms: 0.56
  Number of scatterers: 14558
  At special positions: 0
  Unit cell: (97.52, 116.6, 189.74, 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      17     16.00
     P     348     15.00
     O    3393      8.00
     N    2711      7.00
     C    8089      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: 3.20
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 10 sheets defined
      71.5% alpha, 2.6% beta
      157 base pairs and 325 stacking pairs defined.
    Time for finding SS restraints: 7.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    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 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.335A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.572A  pdb=" N   GLN D  44 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 122
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    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: 4.220A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.537A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 122
    Processing helix  chain 'X' and resid 141 through 161
    Processing helix  chain 'X' and resid 163 through 176
    Processing helix  chain 'X' and resid 180 through 189
      removed outlier: 3.554A  pdb=" N   ILE X 184 " --> pdb=" O   SER X 180 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 193 through 211
      Proline residue:  X 202  - end of helix
    Processing helix  chain 'X' and resid 215 through 220
    Processing helix  chain 'X' and resid 238 through 249
    Processing helix  chain 'X' and resid 256 through 268
      removed outlier: 3.681A  pdb=" N   HIS X 262 " --> pdb=" O   GLN X 258 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 270 through 288
      removed outlier: 4.058A  pdb=" N   SER X 288 " --> pdb=" O   LYS X 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.873A  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
      removed outlier: 6.630A  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: 6.964A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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: 6.919A  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: 7.035A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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

    493 hydrogen bonds defined for protein.
    1458 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      379 hydrogen bonds
      758 hydrogen bond angles
      0 basepair planarities
      157 basepair parallelities
      325 stacking parallelities
  Total time for adding SS restraints: 6.65

  Time building geometry restraints manager: 3.83 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: 2787
        1.33 -     1.45: 5064
        1.45 -     1.57: 6948
        1.57 -     1.69: 694
        1.69 -     1.81: 28
  Bond restraints: 15521
  Sorted by residual:
  bond pdb=" C   LEU G 116 "
       pdb=" N   PRO G 117 "
    ideal  model  delta    sigma   weight residual
    1.332  1.213  0.119 1.34e-02 5.57e+03 7.87e+01
  bond pdb=" C   LEU F  22 "
       pdb=" N   ARG F  23 "
    ideal  model  delta    sigma   weight residual
    1.330  1.384 -0.054 1.22e-02 6.72e+03 1.98e+01
  bond pdb=" N   ASN B  25 "
       pdb=" CA  ASN B  25 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.35e+00
  bond pdb=" N   ILE B  26 "
       pdb=" CA  ILE B  26 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.24e-02 6.50e+03 6.55e+00
  bond pdb=" C   ARG A  40 "
       pdb=" N   TYR A  41 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.43e-02 4.89e+03 3.66e+00
  ... (remaining 15516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 22312
        2.38 -     4.76: 108
        4.76 -     7.14: 12
        7.14 -     9.52: 2
        9.52 -    11.90: 1
  Bond angle restraints: 22435
  Sorted by residual:
  angle pdb=" CB  MET X 197 "
        pdb=" CG  MET X 197 "
        pdb=" SD  MET X 197 "
      ideal   model   delta    sigma   weight residual
     112.70  124.60  -11.90 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" CA  GLU X 238 "
        pdb=" CB  GLU X 238 "
        pdb=" CG  GLU X 238 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" O3'  DA I  74 "
        pdb=" C3'  DA I  74 "
        pdb=" C2'  DA I  74 "
      ideal   model   delta    sigma   weight residual
     111.50  116.28   -4.78 1.50e+00 4.44e-01 1.02e+01
  angle pdb=" CB  LYS A  37 "
        pdb=" CG  LYS A  37 "
        pdb=" CD  LYS A  37 "
      ideal   model   delta    sigma   weight residual
     111.30  117.84   -6.54 2.30e+00 1.89e-01 8.09e+00
  angle pdb=" C3'  DT J -88 "
        pdb=" C2'  DT J -88 "
        pdb=" C1'  DT J -88 "
      ideal   model   delta    sigma   weight residual
     101.60   97.56    4.04 1.50e+00 4.44e-01 7.25e+00
  ... (remaining 22430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 6918
       35.91 -    71.82: 1652
       71.82 -   107.73: 18
      107.73 -   143.64: 2
      143.64 -   179.55: 1
  Dihedral angle restraints: 8591
    sinusoidal: 5887
      harmonic: 2704
  Sorted by residual:
  dihedral pdb=" C4'  DC I  20 "
           pdb=" C3'  DC I  20 "
           pdb=" O3'  DC I  20 "
           pdb=" P    DT I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.45  179.55     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J -93 "
           pdb=" C3'  DG J -93 "
           pdb=" O3'  DG J -93 "
           pdb=" P    DG J -92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.86  138.14     1      3.50e+01 8.16e-04 1.37e+01
  dihedral pdb=" C4'  DA I  52 "
           pdb=" C3'  DA I  52 "
           pdb=" O3'  DA I  52 "
           pdb=" P    DA I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.27  135.73     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 8588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 2008
       0.038 -    0.076: 454
       0.076 -    0.114: 74
       0.114 -    0.152: 12
       0.152 -    0.190: 2
  Chirality restraints: 2550
  Sorted by residual:
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.03e-01
  chirality pdb=" CG  LEU X 190 "
            pdb=" CB  LEU X 190 "
            pdb=" CD1 LEU X 190 "
            pdb=" CD2 LEU X 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.83e-01
  chirality pdb=" CA  LEU X 267 "
            pdb=" N   LEU X 267 "
            pdb=" C   LEU X 267 "
            pdb=" CB  LEU X 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 2547 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  22 "    0.022 2.00e-02 2.50e+03   4.48e-02 2.00e+01
        pdb=" C   LEU F  22 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LEU F  22 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ARG F  23 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.033 5.00e-02 4.00e+02   4.98e-02 3.98e+00
        pdb=" N   PRO E  43 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  40 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" C   ARG A  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ARG A  40 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A  41 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 7
        2.28 -     2.93: 5418
        2.93 -     3.59: 21629
        3.59 -     4.24: 41392
        4.24 -     4.90: 59753
  Nonbonded interactions: 128199
  Sorted by model distance:
  nonbonded pdb=" O   SER G 123 "
            pdb=" OP1  DG J -75 "
     model   vdw
     1.622 3.040
  nonbonded pdb=" CD  LYS G 124 "
            pdb=" O3'  DA J -76 "
     model   vdw
     1.932 3.440
  nonbonded pdb=" C   SER G 123 "
            pdb=" OP1  DG J -75 "
     model   vdw
     2.057 3.270
  nonbonded pdb=" NH1 ARG A  26 "
            pdb=" OP1  DA J   2 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.238 3.120
  ... (remaining 128194 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 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 28 through 122)
  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=0.00 max=1.00 mean=0.99
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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     38.430
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4882
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   0.119  15521  Z= 0.230
  Angle     :  0.593  11.899  22435  Z= 0.354
  Chirality :  0.033   0.190   2550
  Planarity :  0.004   0.050   1630
  Dihedral  : 27.409 179.553   6839
  Min Nonbonded Distance : 1.622

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.27 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 911
  helix:  0.14 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.29 (0.33), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP X 277 
 HIS   0.004   0.001   HIS D 106 
 PHE   0.011   0.001   PHE X 187 
 TYR   0.009   0.001   TYR G  57 
 ARG   0.004   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20972 (  872)
  hydrogen bonds       : angle       6.94673 ( 2216)
  covalent geometry    : bond        0.00491 (15521)
  covalent geometry    : angle       0.59320 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 271
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.5202 (mt) cc_final: 0.4916 (mt)
REVERT: F   19 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7445 (ptp-170)
REVERT: F   20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7206 (tppt)
  outliers start: 5
  outliers final: 0
  residues processed: 273
  average time/residue: 0.3108
  time to fit residues: 117.0382
Evaluate side-chains
  135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0270
   chunk 71 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    1.9844

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
C  24 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
E  76 GLN
H  46 HIS
H  81 ASN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.083934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.058901 restraints weight = 98119.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 3.54
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  15521  Z= 0.217
  Angle     :  0.707   7.875  22435  Z= 0.412
  Chirality :  0.039   0.187   2550
  Planarity :  0.006   0.056   1630
  Dihedral  : 30.720 178.006   4949
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.64 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 911
  helix:  1.57 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.22 (0.34), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 277 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.014   0.001   PHE D  67 
 TYR   0.021   0.002   TYR A  54 
 ARG   0.011   0.001   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05035 (  872)
  hydrogen bonds       : angle       3.52830 ( 2216)
  covalent geometry    : bond        0.00480 (15521)
  covalent geometry    : angle       0.70718 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 ILE cc_start: 0.7277 (mt) cc_final: 0.6952 (mp)
REVERT: B   88 TYR cc_start: 0.7952 (m-10) cc_final: 0.7645 (m-80)
REVERT: E  126 LEU cc_start: 0.8272 (tp) cc_final: 0.7993 (tp)
REVERT: F   19 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7454 (ptp-170)
REVERT: G  118 LYS cc_start: 0.7035 (mmpt) cc_final: 0.5922 (tptp)
REVERT: H   90 GLU cc_start: 0.8889 (mp0) cc_final: 0.8177 (mp0)
  outliers start: 21
  outliers final: 8
  residues processed: 164
  average time/residue: 0.2529
  time to fit residues: 60.3861
Evaluate side-chains
  125 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:   20.0000
   chunk 108 optimal weight:   10.9990
   chunk 27 optimal weight:    0.8980
   chunk 110 optimal weight:   40.0000
   chunk 18 optimal weight:    8.9990
   chunk 112 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0570
   chunk 91 optimal weight:   30.0000
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.1300

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

Flipped N/Q/H residues before XYZ refinement:
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.079949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.054962 restraints weight = 94547.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 3.44
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15521  Z= 0.175
  Angle     :  0.630   6.030  22435  Z= 0.375
  Chirality :  0.035   0.206   2550
  Planarity :  0.005   0.049   1630
  Dihedral  : 30.406 179.691   4949
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 21.40 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.27), residues: 911
  helix:  1.75 (0.20), residues: 663
  sheet:  None (None), residues: 0
  loop : -1.20 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 277 
 HIS   0.007   0.001   HIS A 113 
 PHE   0.035   0.002   PHE B  61 
 TYR   0.020   0.001   TYR H  37 
 ARG   0.004   0.000   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  872)
  hydrogen bonds       : angle       3.26605 ( 2216)
  covalent geometry    : bond        0.00374 (15521)
  covalent geometry    : angle       0.63013 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 LYS cc_start: 0.8000 (ptmt) cc_final: 0.7796 (mtmm)
REVERT: B   88 TYR cc_start: 0.8267 (m-10) cc_final: 0.7987 (m-10)
REVERT: E   90 MET cc_start: 0.8858 (mmm) cc_final: 0.8613 (mmt)
REVERT: E  126 LEU cc_start: 0.8727 (tp) cc_final: 0.8504 (tp)
REVERT: F   19 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7309 (ptp-170)
REVERT: F   79 LYS cc_start: 0.8651 (mppt) cc_final: 0.8072 (mtmm)
REVERT: G   64 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: H   56 MET cc_start: 0.8189 (mmm) cc_final: 0.7714 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 136
  average time/residue: 0.2492
  time to fit residues: 49.8394
Evaluate side-chains
  114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0270
   chunk 16 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    2.1844

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.068926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.042862 restraints weight = 93406.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 3.97
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.8843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  15521  Z= 0.223
  Angle     :  0.709   8.606  22435  Z= 0.418
  Chirality :  0.039   0.204   2550
  Planarity :  0.006   0.072   1630
  Dihedral  : 30.850 175.809   4949
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.40 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.28), residues: 911
  helix:  1.82 (0.20), residues: 661
  sheet:  None (None), residues: 0
  loop : -1.43 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP X 277 
 HIS   0.009   0.002   HIS B  75 
 PHE   0.020   0.002   PHE X 194 
 TYR   0.025   0.002   TYR H  37 
 ARG   0.011   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05800 (  872)
  hydrogen bonds       : angle       3.40690 ( 2216)
  covalent geometry    : bond        0.00500 (15521)
  covalent geometry    : angle       0.70874 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8649 (tt0) cc_final: 0.8447 (tm-30)
REVERT: B   63 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7990 (mt-10)
REVERT: B   88 TYR cc_start: 0.8660 (m-10) cc_final: 0.8282 (m-10)
REVERT: C   90 ASP cc_start: 0.8734 (t0) cc_final: 0.8501 (t0)
REVERT: C   92 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8068 (mt-10)
REVERT: F   19 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.7068 (ptp-170)
REVERT: F   20 LYS cc_start: 0.7908 (tppt) cc_final: 0.7636 (tppt)
REVERT: F   59 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9049 (ttmm)
REVERT: F   63 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8377 (mt-10)
REVERT: G   64 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: G   92 GLU cc_start: 0.8886 (mp0) cc_final: 0.8622 (mp0)
REVERT: H   59 MET cc_start: 0.9505 (mmt) cc_final: 0.9270 (mmm)
  outliers start: 19
  outliers final: 5
  residues processed: 153
  average time/residue: 0.3121
  time to fit residues: 66.5090
Evaluate side-chains
  107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 112 optimal weight:    0.0010
   chunk 50 optimal weight:    0.9980
   chunk 96 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0980
   chunk 58 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
H  81 ASN
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.070240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.043398 restraints weight = 91271.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 3.97
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.9078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15521  Z= 0.154
  Angle     :  0.604   8.526  22435  Z= 0.359
  Chirality :  0.034   0.138   2550
  Planarity :  0.004   0.040   1630
  Dihedral  : 30.512 176.633   4949
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 21.15 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.28), residues: 911
  helix:  2.07 (0.20), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.23 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 277 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE X 187 
 TYR   0.013   0.001   TYR H  37 
 ARG   0.007   0.000   ARG G  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  872)
  hydrogen bonds       : angle       3.08879 ( 2216)
  covalent geometry    : bond        0.00330 (15521)
  covalent geometry    : angle       0.60424 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8365 (mpp) cc_final: 0.7443 (mpp)
REVERT: B   59 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8502 (mtpt)
REVERT: B   63 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: B   88 TYR cc_start: 0.8679 (m-10) cc_final: 0.8319 (m-10)
REVERT: C   90 ASP cc_start: 0.8534 (t0) cc_final: 0.8140 (t0)
REVERT: C   92 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8178 (mt-10)
REVERT: D  102 GLU cc_start: 0.8929 (mp0) cc_final: 0.8713 (mp0)
REVERT: D  113 LYS cc_start: 0.9285 (mtmm) cc_final: 0.8714 (mtmm)
REVERT: E   59 GLU cc_start: 0.7864 (pm20) cc_final: 0.7576 (pm20)
REVERT: E  120 MET cc_start: 0.8068 (mmm) cc_final: 0.7539 (mtt)
REVERT: F   19 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7184 (ptp-170)
REVERT: F   63 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8331 (mt-10)
REVERT: G   41 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8269 (mm-30)
REVERT: G   64 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7907 (tm-30)
REVERT: G   92 GLU cc_start: 0.8841 (mp0) cc_final: 0.8436 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 123
  average time/residue: 0.2784
  time to fit residues: 49.2088
Evaluate side-chains
  104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain G residue  123 SER
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 86 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 120 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 110 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 52 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 113 HIS
F  93 GLN
G  84 GLN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.061814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033882 restraints weight = 96731.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 3.38
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          1.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  15521  Z= 0.315
  Angle     :  0.745   7.720  22435  Z= 0.437
  Chirality :  0.042   0.240   2550
  Planarity :  0.006   0.050   1630
  Dihedral  : 31.617 178.153   4949
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.15 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.27), residues: 911
  helix:  1.75 (0.20), residues: 663
  sheet:  None (None), residues: 0
  loop : -1.46 (0.33), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 277 
 HIS   0.006   0.002   HIS C  31 
 PHE   0.018   0.002   PHE X 194 
 TYR   0.018   0.002   TYR H  37 
 ARG   0.007   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06939 (  872)
  hydrogen bonds       : angle       3.69942 ( 2216)
  covalent geometry    : bond        0.00713 (15521)
  covalent geometry    : angle       0.74544 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8775 (tp30)
REVERT: B   63 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8063 (mt-10)
REVERT: B   88 TYR cc_start: 0.9036 (m-10) cc_final: 0.8625 (m-10)
REVERT: C   90 ASP cc_start: 0.8827 (t0) cc_final: 0.8579 (t0)
REVERT: E   59 GLU cc_start: 0.8345 (pm20) cc_final: 0.8066 (pm20)
REVERT: F   59 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9217 (ttmm)
REVERT: F   63 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8390 (mt-10)
REVERT: F   79 LYS cc_start: 0.9230 (mppt) cc_final: 0.8918 (mmmm)
REVERT: G   56 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8909 (tm-30)
REVERT: G   64 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: G   92 GLU cc_start: 0.9010 (mp0) cc_final: 0.8456 (mp0)
REVERT: H   90 GLU cc_start: 0.9004 (mp0) cc_final: 0.8129 (mp0)
  outliers start: 21
  outliers final: 11
  residues processed: 134
  average time/residue: 0.2902
  time to fit residues: 54.5213
Evaluate side-chains
  114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain G residue  123 SER
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 91 optimal weight:   30.0000
   chunk 122 optimal weight:    6.9990
   chunk 105 optimal weight:    8.9990
   chunk 74 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.062519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.034762 restraints weight = 92942.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 3.40
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          1.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15521  Z= 0.190
  Angle     :  0.635   9.997  22435  Z= 0.375
  Chirality :  0.035   0.136   2550
  Planarity :  0.004   0.040   1630
  Dihedral  : 31.213 175.460   4949
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 22.93 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.28), residues: 911
  helix:  2.07 (0.20), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.32 (0.33), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X 207 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.011   0.001   PHE X 187 
 TYR   0.015   0.001   TYR B  88 
 ARG   0.003   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  872)
  hydrogen bonds       : angle       3.20695 ( 2216)
  covalent geometry    : bond        0.00421 (15521)
  covalent geometry    : angle       0.63479 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8713 (tp30)
REVERT: B   63 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B   88 TYR cc_start: 0.8928 (m-10) cc_final: 0.8366 (m-10)
REVERT: C   90 ASP cc_start: 0.8740 (t0) cc_final: 0.8363 (t0)
REVERT: C   92 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: D   68 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: E   59 GLU cc_start: 0.8210 (pm20) cc_final: 0.7998 (pm20)
REVERT: F   59 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9094 (ttmm)
REVERT: F   79 LYS cc_start: 0.9172 (mppt) cc_final: 0.8920 (mmmm)
REVERT: G   64 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: G   91 GLU cc_start: 0.8630 (pm20) cc_final: 0.8426 (pm20)
REVERT: G   92 GLU cc_start: 0.8950 (mp0) cc_final: 0.8403 (mp0)
REVERT: H   90 GLU cc_start: 0.9020 (mp0) cc_final: 0.8188 (mp0)
  outliers start: 13
  outliers final: 3
  residues processed: 130
  average time/residue: 0.2915
  time to fit residues: 53.3988
Evaluate side-chains
  103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   59 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.063376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.035692 restraints weight = 91743.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 3.27
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          1.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15521  Z= 0.157
  Angle     :  0.610  10.554  22435  Z= 0.362
  Chirality :  0.034   0.203   2550
  Planarity :  0.004   0.041   1630
  Dihedral  : 30.795 175.289   4949
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 23.44 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.28), residues: 911
  helix:  2.14 (0.20), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.25 (0.33), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP X 207 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.014   0.001   PHE X 194 
 TYR   0.013   0.001   TYR H  37 
 ARG   0.003   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  872)
  hydrogen bonds       : angle       3.11084 ( 2216)
  covalent geometry    : bond        0.00341 (15521)
  covalent geometry    : angle       0.61012 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8612 (mm-30)
REVERT: B   59 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8246 (ttmm)
REVERT: B   63 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8038 (mp0)
REVERT: C   90 ASP cc_start: 0.8669 (t0) cc_final: 0.8269 (t0)
REVERT: C   92 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: E   65 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9292 (mp)
REVERT: F   59 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9079 (ttmm)
REVERT: F   63 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8422 (mt-10)
REVERT: F   79 LYS cc_start: 0.9147 (mppt) cc_final: 0.8938 (mmmm)
REVERT: G   64 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7683 (tm-30)
REVERT: G   91 GLU cc_start: 0.8605 (pm20) cc_final: 0.8378 (pm20)
REVERT: G   92 GLU cc_start: 0.8947 (mp0) cc_final: 0.8321 (mp0)
REVERT: H   73 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: H   90 GLU cc_start: 0.9026 (mp0) cc_final: 0.8318 (mp0)
  outliers start: 7
  outliers final: 1
  residues processed: 116
  average time/residue: 0.2773
  time to fit residues: 46.3211
Evaluate side-chains
  108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   59 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.062767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.034895 restraints weight = 92141.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 3.31
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          1.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15521  Z= 0.185
  Angle     :  0.625   9.919  22435  Z= 0.367
  Chirality :  0.034   0.239   2550
  Planarity :  0.004   0.042   1630
  Dihedral  : 30.850 174.783   4949
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 24.46 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.28), residues: 911
  helix:  2.20 (0.20), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.15 (0.34), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 277 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE X 187 
 TYR   0.033   0.002   TYR B  88 
 ARG   0.005   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  872)
  hydrogen bonds       : angle       3.16615 ( 2216)
  covalent geometry    : bond        0.00409 (15521)
  covalent geometry    : angle       0.62514 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8621 (tp30)
REVERT: B   59 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8534 (tttp)
REVERT: B   63 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8095 (mt-10)
REVERT: B   88 TYR cc_start: 0.8820 (m-10) cc_final: 0.8582 (m-10)
REVERT: C   90 ASP cc_start: 0.8665 (t0) cc_final: 0.8255 (t0)
REVERT: C   92 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8267 (mt-10)
REVERT: D   31 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8594 (ptpp)
REVERT: E   59 GLU cc_start: 0.8258 (pm20) cc_final: 0.8054 (pm20)
REVERT: G   64 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: G   91 GLU cc_start: 0.8582 (pm20) cc_final: 0.8355 (pm20)
REVERT: G   92 GLU cc_start: 0.8917 (mp0) cc_final: 0.8353 (mp0)
REVERT: H   73 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8543 (mm-30)
  outliers start: 7
  outliers final: 1
  residues processed: 113
  average time/residue: 0.2808
  time to fit residues: 45.6061
Evaluate side-chains
  102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 118 optimal weight:    9.9990
   chunk 84 optimal weight:    8.9990
   chunk 119 optimal weight:    0.0570
   chunk 121 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.3304

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.062180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.035017 restraints weight = 92882.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.81
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          1.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15521  Z= 0.187
  Angle     :  0.634   9.758  22435  Z= 0.370
  Chirality :  0.035   0.228   2550
  Planarity :  0.005   0.097   1630
  Dihedral  : 30.818 174.452   4949
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 23.95 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.27), residues: 911
  helix:  2.14 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.14 (0.33), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 207 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE D  67 
 TYR   0.049   0.002   TYR B  88 
 ARG   0.008   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  872)
  hydrogen bonds       : angle       3.21649 ( 2216)
  covalent geometry    : bond        0.00412 (15521)
  covalent geometry    : angle       0.63359 (22435)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8662 (tp30)
REVERT: B   63 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8100 (mp0)
REVERT: B   88 TYR cc_start: 0.8886 (m-10) cc_final: 0.8534 (m-10)
REVERT: C   90 ASP cc_start: 0.8697 (t0) cc_final: 0.8329 (t0)
REVERT: C   92 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8427 (mt-10)
REVERT: D   31 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8671 (ptpp)
REVERT: E   59 GLU cc_start: 0.8281 (pm20) cc_final: 0.8071 (pm20)
REVERT: F   59 LYS cc_start: 0.9498 (ttmm) cc_final: 0.9081 (ttpp)
REVERT: F   63 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8315 (mt-10)
REVERT: G   64 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: G   91 GLU cc_start: 0.8606 (pm20) cc_final: 0.8380 (pm20)
REVERT: G   92 GLU cc_start: 0.8917 (mp0) cc_final: 0.8374 (mp0)
REVERT: H   73 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8569 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 105
  average time/residue: 0.2809
  time to fit residues: 42.3272
Evaluate side-chains
  102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 113 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 218 GLN
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.061136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.033805 restraints weight = 93565.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.38
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          1.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  15521  Z= 0.213
  Angle     :  0.643   9.698  22435  Z= 0.376
  Chirality :  0.036   0.233   2550
  Planarity :  0.005   0.083   1630
  Dihedral  : 30.939 174.032   4949
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 24.20 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.28), residues: 911
  helix:  2.22 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.13 (0.34), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 277 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.035   0.002   TYR B  88 
 ARG   0.004   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  872)
  hydrogen bonds       : angle       3.23655 ( 2216)
  covalent geometry    : bond        0.00477 (15521)
  covalent geometry    : angle       0.64289 (22435)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6921.51 seconds
wall clock time: 120 minutes 9.02 seconds (7209.02 seconds total)