Starting phenix.real_space_refine
on Tue Jul 29 17:14:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6px1_20516/07_2025/6px1_20516.cif"
  }
  resolution = 3.3
  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=   0.007
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     290      5.49       5
     S      12      5.16       5
     C    6594      2.51       5
     N    2249      2.21       5
     O    2792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11937
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 792
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 752
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 792
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 752
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 7.67, per 1000 atoms: 0.64
  Number of scatterers: 11937
  At special positions: 0
  Unit cell: (73.84, 117.52, 114.4, 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      12     16.00
     P     290     15.00
     O    2792      8.00
     N    2249      7.00
     C    6594      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: 2.93
  Conformation dependent library (CDL) restraints added in 936.0 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      70.9% alpha, 3.2% beta
      143 base pairs and 274 stacking pairs defined.
    Time for finding SS restraints: 6.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.672A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.668A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.578A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.613A  pdb=" N   ILE C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.553A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 102 through 120
      removed outlier: 3.835A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.694A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    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
      removed outlier: 3.764A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'G' and resid 17 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.339A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE G  62 " --> pdb=" O   LEU G  58 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.530A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.612A  pdb=" N   LEU G 116 " --> pdb=" O   SER G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.521A  pdb=" N   ARG H  76 " --> pdb=" O   GLY H  72 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 102 through 120
      removed outlier: 3.863A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.765A  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: 6.412A  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: 7.154A  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: 6.904A  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: 7.272A  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

    376 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      274 stacking parallelities
  Total time for adding SS restraints: 4.38

  Time building geometry restraints manager: 3.58 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: 2040
        1.33 -     1.45: 4253
        1.45 -     1.57: 5847
        1.57 -     1.68: 578
        1.68 -     1.80: 22
  Bond restraints: 12740
  Sorted by residual:
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.12e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.10e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.485 -0.063 3.00e-02 1.11e+03 4.40e+00
  bond pdb=" CG1 ILE D  58 "
       pdb=" CD1 ILE D  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.437  0.076 3.90e-02 6.57e+02 3.79e+00
  bond pdb=" CG1 ILE H  58 "
       pdb=" CD1 ILE H  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.439  0.074 3.90e-02 6.57e+02 3.64e+00
  ... (remaining 12735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 17527
        1.85 -     3.70: 853
        3.70 -     5.55: 44
        5.55 -     7.40: 19
        7.40 -     9.25: 4
  Bond angle restraints: 18447
  Sorted by residual:
  angle pdb=" C   GLU G  64 "
        pdb=" CA  GLU G  64 "
        pdb=" CB  GLU G  64 "
      ideal   model   delta    sigma   weight residual
     110.90  102.08    8.82 1.58e+00 4.01e-01 3.12e+01
  angle pdb=" N   GLU D  32 "
        pdb=" CA  GLU D  32 "
        pdb=" C   GLU D  32 "
      ideal   model   delta    sigma   weight residual
     108.58  117.83   -9.25 1.82e+00 3.02e-01 2.58e+01
  angle pdb=" C3'  DC J 126 "
        pdb=" O3'  DC J 126 "
        pdb=" P    DC J 127 "
      ideal   model   delta    sigma   weight residual
     120.20  126.32   -6.12 1.50e+00 4.44e-01 1.66e+01
  angle pdb=" C3'  DG J  94 "
        pdb=" O3'  DG J  94 "
        pdb=" P    DG J  95 "
      ideal   model   delta    sigma   weight residual
     120.20  126.09   -5.89 1.50e+00 4.44e-01 1.54e+01
  angle pdb=" N   ARG D  30 "
        pdb=" CA  ARG D  30 "
        pdb=" C   ARG D  30 "
      ideal   model   delta    sigma   weight residual
     109.71  114.76   -5.05 1.41e+00 5.03e-01 1.28e+01
  ... (remaining 18442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 5436
       35.51 -    71.02: 1476
       71.02 -   106.54: 5
      106.54 -   142.05: 0
      142.05 -   177.56: 3
  Dihedral angle restraints: 6920
    sinusoidal: 4738
      harmonic: 2182
  Sorted by residual:
  dihedral pdb=" CA  PRO G 117 "
           pdb=" C   PRO G 117 "
           pdb=" N   LYS G 118 "
           pdb=" CA  LYS G 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.87  -25.13     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  LYS D  31 "
           pdb=" C   LYS D  31 "
           pdb=" N   GLU D  32 "
           pdb=" CA  GLU D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.56 -177.56     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 6917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1618
       0.056 -    0.112: 410
       0.112 -    0.168: 56
       0.168 -    0.224: 11
       0.224 -    0.280: 3
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  THR A  45 "
            pdb=" N   THR A  45 "
            pdb=" C   THR A  45 "
            pdb=" CB  THR A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" C3'  DC J 126 "
            pdb=" C4'  DC J 126 "
            pdb=" O3'  DC J 126 "
            pdb=" C2'  DC J 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.44   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  68 "   -0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        pdb=" C   GLU D  68 "    0.076 2.00e-02 2.50e+03
        pdb=" O   GLU D  68 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG D  69 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F  64 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   ASN F  64 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASN F  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL F  65 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F  80 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   THR F  80 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   THR F  80 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL F  81 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1790
        2.76 -     3.30: 9452
        3.30 -     3.83: 23879
        3.83 -     4.37: 28890
        4.37 -     4.90: 40918
  Nonbonded interactions: 104929
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OE1 GLN F  93 "
            pdb=" NH2 ARG F  95 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.329 3.040
  ... (remaining 104924 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 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:             0.600
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     34.770
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  12740  Z= 0.270
  Angle     :  0.867   9.252  18447  Z= 0.524
  Chirality :  0.050   0.280   2098
  Planarity :  0.008   0.068   1330
  Dihedral  : 28.550 177.562   5512
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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: -2.98 (0.24), residues: 736
  helix: -1.77 (0.18), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.02 (0.34), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.019   0.003   PHE C  25 
 TYR   0.024   0.003   TYR E  41 
 ARG   0.014   0.001   ARG F  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09859 (  744)
  hydrogen bonds       : angle       4.03200 ( 1849)
  covalent geometry    : bond        0.00622 (12740)
  covalent geometry    : angle       0.86723 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.887 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8710 (m-40) cc_final: 0.8491 (m-40)
REVERT: F   35 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8052 (mtm110)
REVERT: G   42 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.8052 (mtm180)
REVERT: G   94 ASN cc_start: 0.8630 (t0) cc_final: 0.8325 (t0)
REVERT: H   87 THR cc_start: 0.8363 (p) cc_final: 0.8141 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.4443
  time to fit residues: 90.1169
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0070
   chunk 58 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
D  92 GLN
E  68 GLN
E 113 HIS
F  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.144822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.101512 restraints weight = 16974.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.49
r_work: 0.3113 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12740  Z= 0.165
  Angle     :  0.578   9.944  18447  Z= 0.349
  Chirality :  0.034   0.181   2098
  Planarity :  0.005   0.052   1330
  Dihedral  : 31.003 174.126   4008
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.16 %
    Favored  : 88.89 %
  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: -0.40 (0.29), residues: 736
  helix:  0.23 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.42 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.009   0.001   TYR A  54 
 ARG   0.004   0.000   ARG F  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  744)
  hydrogen bonds       : angle       2.83432 ( 1849)
  covalent geometry    : bond        0.00363 (12740)
  covalent geometry    : angle       0.57811 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 138
  time to evaluate  : 0.841 
Fit side-chains
REVERT: B   72 TYR cc_start: 0.8960 (m-80) cc_final: 0.8671 (m-80)
REVERT: D   83 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.8197 (mmt90)
REVERT: E   59 GLU cc_start: 0.8014 (mp0) cc_final: 0.7693 (mp0)
REVERT: E   73 GLU cc_start: 0.7822 (tt0) cc_final: 0.7581 (tt0)
REVERT: F   25 ASN cc_start: 0.8822 (m110) cc_final: 0.8601 (m-40)
REVERT: G   42 ARG cc_start: 0.8336 (ptp-170) cc_final: 0.7948 (mtm180)
  outliers start: 6
  outliers final: 2
  residues processed: 138
  average time/residue: 0.3667
  time to fit residues: 64.6753
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.1980
   chunk 24 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  75 HIS
C  68 ASN
C  73 ASN
D  81 ASN
D  92 GLN
E  76 GLN
F  75 HIS
G 104 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.142830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.099916 restraints weight = 17296.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.48
r_work: 0.3091 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12740  Z= 0.189
  Angle     :  0.571   9.668  18447  Z= 0.343
  Chirality :  0.035   0.173   2098
  Planarity :  0.004   0.048   1330
  Dihedral  : 31.012 172.791   4008
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.90 %
    Favored  : 86.35 %
  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:  0.80 (0.30), residues: 736
  helix:  1.13 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.008   0.001   TYR D  37 
 ARG   0.003   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  744)
  hydrogen bonds       : angle       2.66640 ( 1849)
  covalent geometry    : bond        0.00427 (12740)
  covalent geometry    : angle       0.57054 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8131 (ttpp)
REVERT: A   59 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7668 (pm20)
REVERT: A   87 SER cc_start: 0.9141 (p) cc_final: 0.8936 (p)
REVERT: B   72 TYR cc_start: 0.8950 (m-80) cc_final: 0.8733 (m-80)
REVERT: E   59 GLU cc_start: 0.8071 (mp0) cc_final: 0.7517 (pm20)
REVERT: E   73 GLU cc_start: 0.7884 (tt0) cc_final: 0.7610 (tt0)
REVERT: F   25 ASN cc_start: 0.8752 (m110) cc_final: 0.8523 (m-40)
REVERT: F   85 ASP cc_start: 0.8417 (m-30) cc_final: 0.8092 (m-30)
REVERT: G   42 ARG cc_start: 0.8379 (ptp-170) cc_final: 0.7956 (mtm180)
REVERT: H   37 TYR cc_start: 0.9192 (m-80) cc_final: 0.8891 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 129
  average time/residue: 0.3860
  time to fit residues: 63.2911
Evaluate side-chains
  130 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN
E  76 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.144040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.101071 restraints weight = 16937.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.46
r_work: 0.3104 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12740  Z= 0.161
  Angle     :  0.543   9.362  18447  Z= 0.328
  Chirality :  0.033   0.165   2098
  Planarity :  0.004   0.047   1330
  Dihedral  : 30.857 175.115   4008
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.70 %
    Favored  : 85.71 %
  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:  1.52 (0.31), residues: 736
  helix:  1.67 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.82 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.009   0.001   TYR D 118 
 ARG   0.002   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  744)
  hydrogen bonds       : angle       2.57767 ( 1849)
  covalent geometry    : bond        0.00358 (12740)
  covalent geometry    : angle       0.54296 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (pm20)
REVERT: D   49 THR cc_start: 0.8995 (m) cc_final: 0.8739 (t)
REVERT: E   73 GLU cc_start: 0.7846 (tt0) cc_final: 0.7572 (tt0)
REVERT: F   25 ASN cc_start: 0.8745 (m110) cc_final: 0.8505 (m-40)
REVERT: F   85 ASP cc_start: 0.8331 (m-30) cc_final: 0.8009 (m-30)
REVERT: G   42 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7946 (mtm180)
REVERT: H   37 TYR cc_start: 0.9182 (m-80) cc_final: 0.8882 (m-80)
REVERT: H   90 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7936 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 127
  average time/residue: 0.3418
  time to fit residues: 56.1169
Evaluate side-chains
  123 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.096660 restraints weight = 17534.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.50
r_work: 0.3053 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  12740  Z= 0.274
  Angle     :  0.619  10.897  18447  Z= 0.361
  Chirality :  0.038   0.173   2098
  Planarity :  0.005   0.042   1330
  Dihedral  : 31.594 175.601   4008
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.33 %
    Favored  : 83.97 %
  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:  1.22 (0.31), residues: 736
  helix:  1.45 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.92 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.012   0.002   PHE C  25 
 TYR   0.019   0.002   TYR D 118 
 ARG   0.003   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  744)
  hydrogen bonds       : angle       2.81877 ( 1849)
  covalent geometry    : bond        0.00632 (12740)
  covalent geometry    : angle       0.61949 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8164 (mp0) cc_final: 0.7886 (pm20)
REVERT: B   85 ASP cc_start: 0.8599 (m-30) cc_final: 0.8334 (m-30)
REVERT: C   71 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8242 (ttp-170)
REVERT: D   90 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7853 (mp0)
REVERT: E   59 GLU cc_start: 0.8060 (mp0) cc_final: 0.7667 (pm20)
REVERT: E   73 GLU cc_start: 0.7967 (tt0) cc_final: 0.7570 (tt0)
REVERT: F   25 ASN cc_start: 0.8760 (m110) cc_final: 0.8492 (m-40)
REVERT: F   85 ASP cc_start: 0.8386 (m-30) cc_final: 0.8115 (m-30)
REVERT: H   31 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8205 (mptt)
REVERT: H   54 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8294 (mmtt)
REVERT: H   90 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7909 (mp0)
REVERT: H  113 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8400 (ttpp)
  outliers start: 17
  outliers final: 12
  residues processed: 135
  average time/residue: 0.3504
  time to fit residues: 61.4580
Evaluate side-chains
  137 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   71 ARG
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  120 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.143349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.100941 restraints weight = 17775.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.44
r_work: 0.3139 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12740  Z= 0.145
  Angle     :  0.541  10.860  18447  Z= 0.323
  Chirality :  0.032   0.160   2098
  Planarity :  0.004   0.044   1330
  Dihedral  : 30.702 179.104   4008
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.92 %
    Favored  : 83.65 %
  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:  2.08 (0.31), residues: 736
  helix:  2.10 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.70 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.012   0.001   PHE E  78 
 TYR   0.009   0.001   TYR H  37 
 ARG   0.007   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  744)
  hydrogen bonds       : angle       2.54216 ( 1849)
  covalent geometry    : bond        0.00314 (12740)
  covalent geometry    : angle       0.54146 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7811 (pm20)
REVERT: A  133 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: D   49 THR cc_start: 0.8986 (m) cc_final: 0.8761 (t)
REVERT: D   90 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7882 (mp0)
REVERT: E   59 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7766 (pm20)
REVERT: E   73 GLU cc_start: 0.7938 (tt0) cc_final: 0.7565 (tt0)
REVERT: F   25 ASN cc_start: 0.8736 (m110) cc_final: 0.8488 (m-40)
REVERT: F   85 ASP cc_start: 0.8290 (m-30) cc_final: 0.7954 (m-30)
REVERT: G   42 ARG cc_start: 0.8302 (ptp-170) cc_final: 0.7914 (mtm180)
REVERT: H   90 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7925 (mp0)
  outliers start: 9
  outliers final: 2
  residues processed: 129
  average time/residue: 0.3357
  time to fit residues: 57.0113
Evaluate side-chains
  123 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.143205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.100377 restraints weight = 17860.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.43
r_work: 0.3117 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12740  Z= 0.179
  Angle     :  0.555  10.854  18447  Z= 0.329
  Chirality :  0.034   0.161   2098
  Planarity :  0.004   0.043   1330
  Dihedral  : 30.859 179.525   4008
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.71 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.15 (0.31), residues: 736
  helix:  2.14 (0.23), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.61 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.019   0.001   TYR D 118 
 ARG   0.006   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  744)
  hydrogen bonds       : angle       2.54588 ( 1849)
  covalent geometry    : bond        0.00403 (12740)
  covalent geometry    : angle       0.55493 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7831 (pm20)
REVERT: D   49 THR cc_start: 0.9002 (m) cc_final: 0.8764 (t)
REVERT: D   90 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7853 (mp0)
REVERT: E   59 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7707 (pm20)
REVERT: E   73 GLU cc_start: 0.7954 (tt0) cc_final: 0.7596 (tt0)
REVERT: F   25 ASN cc_start: 0.8748 (m110) cc_final: 0.8502 (m-40)
REVERT: F   85 ASP cc_start: 0.8263 (m-30) cc_final: 0.7950 (m-30)
REVERT: G   42 ARG cc_start: 0.8363 (ptp-170) cc_final: 0.7966 (mtm180)
REVERT: H   54 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8318 (mmtt)
REVERT: H   90 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7882 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 124
  average time/residue: 0.3300
  time to fit residues: 54.0880
Evaluate side-chains
  130 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.141661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.098936 restraints weight = 17893.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.44
r_work: 0.3093 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12740  Z= 0.196
  Angle     :  0.566  12.047  18447  Z= 0.333
  Chirality :  0.035   0.163   2098
  Planarity :  0.004   0.042   1330
  Dihedral  : 31.078 178.897   4008
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.19 %
    Favored  : 81.59 %
  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:  2.11 (0.31), residues: 736
  helix:  2.16 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.63 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.019   0.001   TYR D 118 
 ARG   0.006   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  744)
  hydrogen bonds       : angle       2.60833 ( 1849)
  covalent geometry    : bond        0.00446 (12740)
  covalent geometry    : angle       0.56574 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7765 (pm20)
REVERT: A  133 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7487 (mt-10)
REVERT: D   49 THR cc_start: 0.9006 (m) cc_final: 0.8772 (t)
REVERT: D   90 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7835 (mp0)
REVERT: E   59 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7683 (pm20)
REVERT: F   25 ASN cc_start: 0.8768 (m110) cc_final: 0.8511 (m-40)
REVERT: F   85 ASP cc_start: 0.8254 (m-30) cc_final: 0.7932 (m-30)
REVERT: G   42 ARG cc_start: 0.8399 (ptp-170) cc_final: 0.7983 (mtm180)
REVERT: H   54 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8325 (mmtt)
REVERT: H   90 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7849 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 125
  average time/residue: 0.3338
  time to fit residues: 54.6147
Evaluate side-chains
  131 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 84 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  24 GLN
D  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.144533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.101892 restraints weight = 17813.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.43
r_work: 0.3140 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12740  Z= 0.145
  Angle     :  0.541  12.096  18447  Z= 0.321
  Chirality :  0.033   0.156   2098
  Planarity :  0.004   0.043   1330
  Dihedral  : 30.732 179.794   4008
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.30 %
    Favored  : 80.95 %
  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:  2.47 (0.31), residues: 736
  helix:  2.40 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.50 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.015   0.001   TYR D 118 
 ARG   0.006   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  744)
  hydrogen bonds       : angle       2.49950 ( 1849)
  covalent geometry    : bond        0.00317 (12740)
  covalent geometry    : angle       0.54127 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7785 (pm20)
REVERT: A   90 MET cc_start: 0.8473 (tpp) cc_final: 0.8125 (mmp)
REVERT: A  133 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7579 (mt-10)
REVERT: D   49 THR cc_start: 0.8995 (m) cc_final: 0.8769 (t)
REVERT: D   56 MET cc_start: 0.8862 (tpp) cc_final: 0.8388 (tpt)
REVERT: D   90 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7803 (mp0)
REVERT: E   59 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7637 (pm20)
REVERT: E   73 GLU cc_start: 0.7837 (tt0) cc_final: 0.7557 (tt0)
REVERT: F   25 ASN cc_start: 0.8762 (m110) cc_final: 0.8301 (m-40)
REVERT: F   85 ASP cc_start: 0.8331 (m-30) cc_final: 0.7989 (m-30)
REVERT: G   42 ARG cc_start: 0.8373 (ptp-170) cc_final: 0.7943 (mtm180)
REVERT: H   54 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8336 (mmtt)
REVERT: H   87 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8257 (t)
REVERT: H   90 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7924 (mp0)
  outliers start: 11
  outliers final: 5
  residues processed: 124
  average time/residue: 0.3203
  time to fit residues: 52.4095
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.145184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102739 restraints weight = 17663.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.41
r_work: 0.3140 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12740  Z= 0.149
  Angle     :  0.547  12.754  18447  Z= 0.323
  Chirality :  0.033   0.157   2098
  Planarity :  0.004   0.043   1330
  Dihedral  : 30.734 179.639   4008
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.98 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.58 (0.31), residues: 736
  helix:  2.47 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.42 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.017   0.001   TYR D 118 
 ARG   0.007   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  744)
  hydrogen bonds       : angle       2.49999 ( 1849)
  covalent geometry    : bond        0.00327 (12740)
  covalent geometry    : angle       0.54717 (18447)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 2.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7764 (pm20)
REVERT: A   90 MET cc_start: 0.8478 (tpp) cc_final: 0.8137 (mmp)
REVERT: A  133 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: D   49 THR cc_start: 0.8984 (m) cc_final: 0.8750 (t)
REVERT: D   56 MET cc_start: 0.8845 (tpp) cc_final: 0.8380 (tpt)
REVERT: D   90 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7822 (mp0)
REVERT: E   59 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7640 (pm20)
REVERT: F   25 ASN cc_start: 0.8759 (m110) cc_final: 0.8511 (m-40)
REVERT: F   85 ASP cc_start: 0.8278 (m-30) cc_final: 0.7959 (m-30)
REVERT: G   42 ARG cc_start: 0.8369 (ptp-170) cc_final: 0.7948 (mtm180)
REVERT: H   54 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8337 (mmtt)
REVERT: H   56 MET cc_start: 0.8864 (tpp) cc_final: 0.8401 (tpt)
REVERT: H   87 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8247 (t)
REVERT: H   90 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7937 (mp0)
  outliers start: 11
  outliers final: 5
  residues processed: 126
  average time/residue: 0.4787
  time to fit residues: 80.2414
Evaluate side-chains
  128 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.144528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.101873 restraints weight = 17652.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.44
r_work: 0.3140 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12740  Z= 0.159
  Angle     :  0.549  12.723  18447  Z= 0.324
  Chirality :  0.033   0.157   2098
  Planarity :  0.004   0.043   1330
  Dihedral  : 30.738 179.628   4008
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.46 %
    Favored  : 80.95 %
  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:  2.59 (0.31), residues: 736
  helix:  2.48 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.42 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.021   0.001   TYR H  39 
 ARG   0.007   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  744)
  hydrogen bonds       : angle       2.51033 ( 1849)
  covalent geometry    : bond        0.00354 (12740)
  covalent geometry    : angle       0.54914 (18447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5948.47 seconds
wall clock time: 107 minutes 6.09 seconds (6426.09 seconds total)