Starting phenix.real_space_refine
on Tue Jul 29 05:50:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2025/7pii_13437_neut.cif"
  }
  resolution = 2.68
  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=   0.002
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     244      5.49       5
     S       8      5.16       5
     C    6321      2.51       5
     N    2070      2.21       5
     O    2549      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11192
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 799
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 755
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 770
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    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: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 784
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2506
          Classifications: {'DNA': 122}
          Link IDs: {'rna3p': 121}
    Chain: "J"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2514
          Classifications: {'DNA': 123}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 122}
    Chain: "K"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 178
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 19}
    Chain: "L"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 185
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 1, 'TRANS': 20}
  Time building chain proxies: 8.15, per 1000 atoms: 0.73
  Number of scatterers: 11192
  At special positions: 0
  Unit cell: (80.607, 114.678, 123.819, 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       8     16.00
     P     244     15.00
     O    2549      8.00
     N    2070      7.00
     C    6321      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: 2.84
  Conformation dependent library (CDL) restraints added in 958.1 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      68.9% alpha, 2.6% beta
      121 base pairs and 220 stacking pairs defined.
    Time for finding SS restraints: 5.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.629A  pdb=" N   LYS A  49 " --> pdb=" O   GLN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.618A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 138
      removed outlier: 5.628A  pdb=" N   LEU A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   GLU A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    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: 4.409A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (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 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 47 through 55
    Processing helix  chain 'E' and resid 63 through 78
    Processing helix  chain 'E' and resid 87 through 116
    Processing helix  chain 'E' and resid 122 through 134
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.479A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.727A  pdb=" N   ASN A  85 " --> 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 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.452A  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 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.916A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.180A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'L' and resid 516 through 517

    408 hydrogen bonds defined for protein.
    1221 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      282 hydrogen bonds
      564 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      220 stacking parallelities
  Total time for adding SS restraints: 4.04

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1668
        1.32 -     1.45: 4128
        1.45 -     1.57: 5598
        1.57 -     1.69: 487
        1.69 -     1.81: 14
  Bond restraints: 11895
  Sorted by residual:
  bond pdb=" N   ILE D  54 "
       pdb=" CA  ILE D  54 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.18e-02 7.18e+03 1.04e+01
  bond pdb=" N   VAL K 517 "
       pdb=" CA  VAL K 517 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.20e-02 6.94e+03 9.56e+00
  bond pdb=" N   VAL K 533 "
       pdb=" CA  VAL K 533 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.22e+00
  bond pdb=" N   THR K 518 "
       pdb=" CA  THR K 518 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.17e-02 7.31e+03 9.20e+00
  bond pdb=" N   VAL K 532 "
       pdb=" CA  VAL K 532 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 1.24e-02 6.50e+03 8.70e+00
  ... (remaining 11890 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 16152
        1.63 -     3.27: 871
        3.27 -     4.90: 83
        4.90 -     6.54: 9
        6.54 -     8.17: 1
  Bond angle restraints: 17116
  Sorted by residual:
  angle pdb=" N   LEU F  49 "
        pdb=" CA  LEU F  49 "
        pdb=" C   LEU F  49 "
      ideal   model   delta    sigma   weight residual
     113.18  108.67    4.51 1.21e+00 6.83e-01 1.39e+01
  angle pdb=" N   GLN B  27 "
        pdb=" CA  GLN B  27 "
        pdb=" C   GLN B  27 "
      ideal   model   delta    sigma   weight residual
     113.01  108.59    4.42 1.20e+00 6.94e-01 1.36e+01
  angle pdb=" N   VAL E 119 "
        pdb=" CA  VAL E 119 "
        pdb=" C   VAL E 119 "
      ideal   model   delta    sigma   weight residual
     113.10  109.53    3.57 9.70e-01 1.06e+00 1.36e+01
  angle pdb=" CA  SER K 524 "
        pdb=" C   SER K 524 "
        pdb=" O   SER K 524 "
      ideal   model   delta    sigma   weight residual
     122.37  118.26    4.11 1.15e+00 7.56e-01 1.28e+01
  angle pdb=" N   TYR H  37 "
        pdb=" CA  TYR H  37 "
        pdb=" C   TYR H  37 "
      ideal   model   delta    sigma   weight residual
     113.21  109.43    3.78 1.15e+00 7.56e-01 1.08e+01
  ... (remaining 17111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.25: 5305
       35.25 -    70.50: 1265
       70.50 -   105.75: 23
      105.75 -   141.01: 1
      141.01 -   176.26: 2
  Dihedral angle restraints: 6596
    sinusoidal: 4351
      harmonic: 2245
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.05  -25.95     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  HIS F  75 "
           pdb=" C   HIS F  75 "
           pdb=" N   ALA F  76 "
           pdb=" CA  ALA F  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ARG E 133 "
           pdb=" C   ARG E 133 "
           pdb=" N   GLY E 134 "
           pdb=" CA  GLY E 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.22   21.78     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 6593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1668
       0.063 -    0.126: 252
       0.126 -    0.189: 24
       0.189 -    0.252: 3
       0.252 -    0.315: 1
  Chirality restraints: 1948
  Sorted by residual:
  chirality pdb=" CA  TYR E 110 "
            pdb=" N   TYR E 110 "
            pdb=" C   TYR E 110 "
            pdb=" CB  TYR E 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ARG E  80 "
            pdb=" N   ARG E  80 "
            pdb=" C   ARG E  80 "
            pdb=" CB  ARG E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 1945 not shown)

  Planarity restraints: 1307
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I   5 "    0.029 2.00e-02 2.50e+03   1.40e-02 4.92e+00
        pdb=" N1   DT I   5 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2   DT I   5 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2   DT I   5 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT I   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I   5 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT I   5 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DT I   5 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I   5 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  57 "   -0.029 2.00e-02 2.50e+03   1.27e-02 4.45e+00
        pdb=" N9   DA I  57 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA I  57 "    0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  57 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  57 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA I  57 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 118 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   ARG E 118 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ARG E 118 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL E 119 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1304 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2013
        2.76 -     3.30: 10136
        3.30 -     3.83: 22576
        3.83 -     4.37: 27405
        4.37 -     4.90: 37724
  Nonbonded interactions: 99854
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   SER C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR L 514 "
            pdb=" N   SER L 515 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NH2 ARG E  69 "
            pdb=" OP2  DA I  17 "
     model   vdw
     2.277 3.120
  ... (remaining 99849 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 46 through 139)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 15 through 111)
  selection = (chain 'G' and resid 15 through 111)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'L' and resid 515 through 535)
}

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:                  0.010
  Normalize map: mean=0, sd=1:             4.430
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.170
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:13.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3661
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      :  0.010   0.054  11895  Z= 0.464
  Angle     :  0.776   8.174  17116  Z= 0.492
  Chirality :  0.047   0.315   1948
  Planarity :  0.004   0.038   1307
  Dihedral  : 28.133 176.257   5146
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 13.53 %
    Favored  : 86.16 %
  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: -0.89 (0.27), residues: 759
  helix:  0.24 (0.20), residues: 541
  sheet:  None (None), residues: 0
  loop : -2.63 (0.31), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 531 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.014   0.002   TYR F  51 
 ARG   0.008   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13500 (  690)
  hydrogen bonds       : angle       4.69526 ( 1785)
  covalent geometry    : bond        0.00970 (11895)
  covalent geometry    : angle       0.77623 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  107 GLU cc_start: 0.4059 (mt-10) cc_final: 0.3831 (mt-10)
REVERT: A  137 GLU cc_start: 0.4620 (tt0) cc_final: 0.4236 (tt0)
REVERT: B   44 LYS cc_start: 0.5387 (mtmt) cc_final: 0.4830 (tttt)
REVERT: B   78 ARG cc_start: 0.5414 (mtm-85) cc_final: 0.5186 (mtm110)
REVERT: C   20 ARG cc_start: 0.4966 (ttm110) cc_final: 0.4624 (mtm180)
REVERT: D   71 GLU cc_start: 0.4649 (tm-30) cc_final: 0.4446 (tp30)
REVERT: E   57 SER cc_start: 0.5724 (t) cc_final: 0.5509 (p)
REVERT: E   82 VAL cc_start: 0.4383 (OUTLIER) cc_final: 0.4164 (p)
REVERT: E   83 ASP cc_start: 0.6312 (p0) cc_final: 0.6030 (t70)
REVERT: F   31 LYS cc_start: 0.5009 (mttp) cc_final: 0.4705 (mtpt)
REVERT: F   44 LYS cc_start: 0.5327 (tttt) cc_final: 0.4232 (mttt)
REVERT: F   63 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5168 (mt-10)
REVERT: F   91 LYS cc_start: 0.5476 (tttm) cc_final: 0.5205 (ttpp)
REVERT: G   36 LYS cc_start: 0.5899 (mptt) cc_final: 0.5657 (pttt)
REVERT: G  104 GLN cc_start: 0.5425 (mm-40) cc_final: 0.5119 (mm110)
REVERT: L  525 ARG cc_start: 0.5300 (mtm-85) cc_final: 0.5074 (mtt-85)
  outliers start: 2
  outliers final: 0
  residues processed: 173
  average time/residue: 2.0279
  time to fit residues: 367.5363
Evaluate side-chains
  119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  24 GLN
C  94 ASN
C 104 GLN
D  47 GLN
D  84 ASN
E  87 GLN
E 115 HIS
F  27 GLN
F  75 HIS
F  93 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  94 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.163628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.116533 restraints weight = 12981.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 0.98
r_work: 0.3122 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11895  Z= 0.176
  Angle     :  0.625   7.567  17116  Z= 0.370
  Chirality :  0.036   0.133   1948
  Planarity :  0.004   0.039   1307
  Dihedral  : 30.918 177.513   3648
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.66 %
    Favored  : 78.38 %
  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:  1.05 (0.28), residues: 759
  helix:  1.61 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.73 (0.35), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  47 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.010   0.002   TYR B  51 
 ARG   0.003   0.000   ARG L 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04732 (  690)
  hydrogen bonds       : angle       3.28136 ( 1785)
  covalent geometry    : bond        0.00386 (11895)
  covalent geometry    : angle       0.62509 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.841 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8159 (mttt) cc_final: 0.7938 (tttt)
REVERT: D   46 LYS cc_start: 0.8346 (mmpt) cc_final: 0.7959 (mppt)
REVERT: F   44 LYS cc_start: 0.8738 (tttt) cc_final: 0.7963 (mttt)
REVERT: G   73 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7875 (t0)
REVERT: H   57 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7977 (mtpt)
REVERT: H   68 ASP cc_start: 0.9146 (t0) cc_final: 0.8904 (t70)
REVERT: L  525 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7451 (mtt-85)
  outliers start: 19
  outliers final: 5
  residues processed: 138
  average time/residue: 1.8626
  time to fit residues: 270.0937
Evaluate side-chains
  124 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   57 LYS
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.159604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.112501 restraints weight = 13079.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.00
r_work: 0.3055 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  11895  Z= 0.304
  Angle     :  0.733   8.900  17116  Z= 0.423
  Chirality :  0.044   0.154   1948
  Planarity :  0.006   0.065   1307
  Dihedral  : 31.486 176.004   3647
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.20 %
    Favored  : 77.92 %
  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:  0.97 (0.28), residues: 759
  helix:  1.43 (0.20), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.42 (0.36), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A  47 
 HIS   0.006   0.002   HIS D  49 
 PHE   0.020   0.003   PHE A  78 
 TYR   0.015   0.003   TYR F  51 
 ARG   0.008   0.001   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06349 (  690)
  hydrogen bonds       : angle       3.47563 ( 1785)
  covalent geometry    : bond        0.00699 (11895)
  covalent geometry    : angle       0.73292 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.358 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8131 (mtp85)
REVERT: B   44 LYS cc_start: 0.8176 (mttt) cc_final: 0.7909 (tttt)
REVERT: B   49 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8438 (mt)
REVERT: C   77 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.5716 (ttt-90)
REVERT: E   49 LYS cc_start: 0.8186 (tttp) cc_final: 0.7915 (tmtp)
REVERT: F   44 LYS cc_start: 0.8898 (tttt) cc_final: 0.7930 (mtmt)
REVERT: G   73 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (t0)
REVERT: L  525 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7534 (mtt-85)
  outliers start: 25
  outliers final: 7
  residues processed: 137
  average time/residue: 1.8666
  time to fit residues: 268.9673
Evaluate side-chains
  132 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  532 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 50 optimal weight:    0.3980
   chunk 78 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0060
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.163253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.115963 restraints weight = 12913.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 0.95
r_work: 0.3125 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11895  Z= 0.162
  Angle     :  0.626   7.466  17116  Z= 0.369
  Chirality :  0.036   0.134   1948
  Planarity :  0.004   0.043   1307
  Dihedral  : 31.217 173.902   3647
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.28 %
    Favored  : 78.23 %
  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:  1.68 (0.29), residues: 759
  helix:  1.91 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.98 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.001   PHE E  67 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.009   0.000   ARG K 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04733 (  690)
  hydrogen bonds       : angle       3.27934 ( 1785)
  covalent geometry    : bond        0.00351 (11895)
  covalent geometry    : angle       0.62639 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.881 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8141 (mttt) cc_final: 0.7889 (tttt)
REVERT: C   38 ASN cc_start: 0.7600 (p0) cc_final: 0.7333 (p0)
REVERT: C   61 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8607 (mm-30)
REVERT: C   77 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.5317 (ttt-90)
REVERT: D   46 LYS cc_start: 0.8400 (mmpt) cc_final: 0.7945 (mppt)
REVERT: E   49 LYS cc_start: 0.8154 (tttp) cc_final: 0.7851 (tmtp)
REVERT: F   44 LYS cc_start: 0.8829 (tttt) cc_final: 0.7913 (mttt)
REVERT: H   68 ASP cc_start: 0.9077 (t0) cc_final: 0.8801 (t70)
REVERT: K  525 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7129 (mtt180)
REVERT: L  525 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7474 (mtt-85)
  outliers start: 16
  outliers final: 4
  residues processed: 134
  average time/residue: 1.9977
  time to fit residues: 281.0509
Evaluate side-chains
  125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 32 optimal weight:    0.0040
   chunk 55 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0670
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4530

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.165112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.118044 restraints weight = 13013.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 0.99
r_work: 0.3148 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11895  Z= 0.152
  Angle     :  0.586   6.904  17116  Z= 0.350
  Chirality :  0.034   0.137   1948
  Planarity :  0.004   0.044   1307
  Dihedral  : 30.725 171.551   3647
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.37 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.21 (0.29), residues: 759
  helix:  2.31 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.77 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.010   0.001   TYR B  51 
 ARG   0.005   0.000   ARG K 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04291 (  690)
  hydrogen bonds       : angle       3.14089 ( 1785)
  covalent geometry    : bond        0.00328 (11895)
  covalent geometry    : angle       0.58556 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8009 (mtp85)
REVERT: A  137 GLU cc_start: 0.7636 (tt0) cc_final: 0.7354 (tt0)
REVERT: B   44 LYS cc_start: 0.8158 (mttt) cc_final: 0.7899 (tttt)
REVERT: C   38 ASN cc_start: 0.7558 (p0) cc_final: 0.7293 (p0)
REVERT: C   77 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.5111 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5547 (pt) cc_final: 0.5014 (pp)
REVERT: D   46 LYS cc_start: 0.8379 (mmpt) cc_final: 0.8007 (mppt)
REVERT: E   49 LYS cc_start: 0.8140 (tttp) cc_final: 0.7864 (tmtp)
REVERT: F   44 LYS cc_start: 0.8801 (tttt) cc_final: 0.7916 (mttt)
REVERT: G   73 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7825 (t0)
REVERT: H   68 ASP cc_start: 0.9097 (t0) cc_final: 0.8834 (t70)
REVERT: K  525 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7248 (mtt180)
REVERT: L  525 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7441 (mtt-85)
  outliers start: 17
  outliers final: 5
  residues processed: 135
  average time/residue: 1.9760
  time to fit residues: 280.5720
Evaluate side-chains
  127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.163797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115652 restraints weight = 13096.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.04
r_work: 0.3114 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.176
  Angle     :  0.606   7.513  17116  Z= 0.359
  Chirality :  0.036   0.138   1948
  Planarity :  0.004   0.047   1307
  Dihedral  : 30.764 172.955   3647
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.68 %
    Favored  : 76.67 %
  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:  2.16 (0.29), residues: 759
  helix:  2.24 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.73 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.012   0.002   TYR B  51 
 ARG   0.009   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  690)
  hydrogen bonds       : angle       3.17181 ( 1785)
  covalent geometry    : bond        0.00391 (11895)
  covalent geometry    : angle       0.60592 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8060 (mtp85)
REVERT: B   44 LYS cc_start: 0.8202 (mttt) cc_final: 0.7927 (tttt)
REVERT: C   38 ASN cc_start: 0.7667 (p0) cc_final: 0.7388 (p0)
REVERT: C   77 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5255 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5466 (pt) cc_final: 0.4944 (pp)
REVERT: D   46 LYS cc_start: 0.8379 (mmpt) cc_final: 0.7938 (mppt)
REVERT: E   49 LYS cc_start: 0.8141 (tttp) cc_final: 0.7849 (tmtp)
REVERT: F   44 LYS cc_start: 0.8811 (tttt) cc_final: 0.7910 (mttt)
REVERT: G   73 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (t0)
REVERT: H   68 ASP cc_start: 0.9150 (t0) cc_final: 0.8913 (t70)
REVERT: K  525 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7206 (mtt180)
REVERT: L  525 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7421 (mtt-85)
  outliers start: 17
  outliers final: 6
  residues processed: 132
  average time/residue: 1.9345
  time to fit residues: 268.6989
Evaluate side-chains
  127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0060
   chunk 20 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
** H  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.164076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.116784 restraints weight = 13195.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.00
r_work: 0.3113 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.168
  Angle     :  0.603   7.483  17116  Z= 0.358
  Chirality :  0.035   0.137   1948
  Planarity :  0.004   0.053   1307
  Dihedral  : 30.751 173.243   3647
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.15 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.18 (0.29), residues: 759
  helix:  2.26 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.72 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.007   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04681 (  690)
  hydrogen bonds       : angle       3.17753 ( 1785)
  covalent geometry    : bond        0.00371 (11895)
  covalent geometry    : angle       0.60344 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8058 (mtp85)
REVERT: A  137 GLU cc_start: 0.7654 (tt0) cc_final: 0.7327 (tt0)
REVERT: B   44 LYS cc_start: 0.8193 (mttt) cc_final: 0.7974 (tttt)
REVERT: C   38 ASN cc_start: 0.7657 (p0) cc_final: 0.7405 (p0)
REVERT: C   77 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5326 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5471 (pt) cc_final: 0.4970 (pp)
REVERT: D   46 LYS cc_start: 0.8369 (mmpt) cc_final: 0.8059 (mppt)
REVERT: E   49 LYS cc_start: 0.8204 (tttp) cc_final: 0.7938 (tmtp)
REVERT: F   44 LYS cc_start: 0.8818 (tttt) cc_final: 0.8008 (mttt)
REVERT: G   73 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7845 (t0)
REVERT: H   68 ASP cc_start: 0.9130 (t0) cc_final: 0.8884 (t70)
REVERT: K  525 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7280 (mtt180)
REVERT: L  525 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7493 (mtt-85)
  outliers start: 17
  outliers final: 11
  residues processed: 131
  average time/residue: 2.0722
  time to fit residues: 285.4076
Evaluate side-chains
  133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.163848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.116614 restraints weight = 13140.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 0.98
r_work: 0.3118 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.176
  Angle     :  0.606   7.473  17116  Z= 0.359
  Chirality :  0.036   0.137   1948
  Planarity :  0.004   0.043   1307
  Dihedral  : 30.717 177.369   3647
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.15 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.29), residues: 759
  helix:  2.21 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.66 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.012   0.002   TYR B  88 
 ARG   0.006   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04775 (  690)
  hydrogen bonds       : angle       3.19262 ( 1785)
  covalent geometry    : bond        0.00393 (11895)
  covalent geometry    : angle       0.60566 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8097 (mtp85)
REVERT: B   44 LYS cc_start: 0.8146 (mttt) cc_final: 0.7908 (tttt)
REVERT: C   38 ASN cc_start: 0.7674 (p0) cc_final: 0.7414 (p0)
REVERT: C   77 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.5285 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5684 (pt) cc_final: 0.5250 (pp)
REVERT: D   46 LYS cc_start: 0.8337 (mmpt) cc_final: 0.7955 (mppt)
REVERT: D   93 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8259 (mp0)
REVERT: E   49 LYS cc_start: 0.8172 (tttp) cc_final: 0.7886 (tmtp)
REVERT: F   44 LYS cc_start: 0.8825 (tttt) cc_final: 0.7959 (mttt)
REVERT: G   73 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7811 (t0)
REVERT: H   68 ASP cc_start: 0.9109 (t0) cc_final: 0.8867 (t70)
REVERT: L  525 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7492 (mtt-85)
  outliers start: 17
  outliers final: 9
  residues processed: 136
  average time/residue: 1.8955
  time to fit residues: 271.2828
Evaluate side-chains
  133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0870
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.164419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117115 restraints weight = 13097.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.00
r_work: 0.3128 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11895  Z= 0.166
  Angle     :  0.603   7.477  17116  Z= 0.358
  Chirality :  0.035   0.137   1948
  Planarity :  0.004   0.063   1307
  Dihedral  : 30.706 177.610   3647
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.77 %
    Favored  : 75.43 %
  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:  2.18 (0.29), residues: 759
  helix:  2.22 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.63 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.008   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04667 (  690)
  hydrogen bonds       : angle       3.19434 ( 1785)
  covalent geometry    : bond        0.00367 (11895)
  covalent geometry    : angle       0.60288 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.977 
Fit side-chains
REVERT: B   44 LYS cc_start: 0.8126 (mttt) cc_final: 0.7880 (tttt)
REVERT: C   38 ASN cc_start: 0.7642 (p0) cc_final: 0.7388 (p0)
REVERT: C   77 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.5293 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5704 (pt) cc_final: 0.5287 (pp)
REVERT: D   46 LYS cc_start: 0.8339 (mmpt) cc_final: 0.7947 (mppt)
REVERT: D   93 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8199 (mp0)
REVERT: E   49 LYS cc_start: 0.8144 (tttp) cc_final: 0.7854 (tmtp)
REVERT: F   44 LYS cc_start: 0.8828 (tttt) cc_final: 0.7935 (mttt)
REVERT: G   73 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7784 (t0)
REVERT: H   68 ASP cc_start: 0.9120 (t0) cc_final: 0.8886 (t70)
REVERT: K  525 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7166 (mtt180)
REVERT: L  525 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7489 (mtt-85)
  outliers start: 18
  outliers final: 11
  residues processed: 131
  average time/residue: 2.0203
  time to fit residues: 277.9514
Evaluate side-chains
  134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0270
   chunk 64 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
F  64 ASN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.163413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116052 restraints weight = 12972.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 0.97
r_work: 0.3106 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11895  Z= 0.187
  Angle     :  0.622   7.644  17116  Z= 0.367
  Chirality :  0.036   0.138   1948
  Planarity :  0.004   0.043   1307
  Dihedral  : 30.748 179.291   3647
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.93 %
    Favored  : 75.27 %
  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:  2.10 (0.29), residues: 759
  helix:  2.15 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.60 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.012   0.002   TYR B  51 
 ARG   0.007   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04989 (  690)
  hydrogen bonds       : angle       3.23059 ( 1785)
  covalent geometry    : bond        0.00422 (11895)
  covalent geometry    : angle       0.62209 (17116)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.401 
Fit side-chains
REVERT: A  133 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8021 (mtp85)
REVERT: B   44 LYS cc_start: 0.8147 (mttt) cc_final: 0.7916 (tttt)
REVERT: C   77 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.5474 (ttt-90)
REVERT: C  111 ILE cc_start: 0.5641 (pt) cc_final: 0.5285 (pp)
REVERT: D   46 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7946 (mppt)
REVERT: E   49 LYS cc_start: 0.8175 (tttp) cc_final: 0.7897 (tmtp)
REVERT: F   44 LYS cc_start: 0.8831 (tttt) cc_final: 0.7965 (mttt)
REVERT: G   73 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7800 (t0)
REVERT: H   68 ASP cc_start: 0.9104 (t0) cc_final: 0.8897 (t70)
REVERT: K  523 ILE cc_start: 0.8239 (mp) cc_final: 0.7939 (mt)
REVERT: K  525 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7150 (mtt180)
REVERT: L  525 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7491 (mtt-85)
  outliers start: 18
  outliers final: 11
  residues processed: 131
  average time/residue: 2.4157
  time to fit residues: 332.0422
Evaluate side-chains
  131 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 17 optimal weight:    0.3980
   chunk 57 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  47 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.163544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.116394 restraints weight = 12943.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 0.97
r_work: 0.3114 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11895  Z= 0.186
  Angle     :  0.620   7.564  17116  Z= 0.366
  Chirality :  0.036   0.138   1948
  Planarity :  0.004   0.046   1307
  Dihedral  : 30.678 178.338   3647
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.55 %
    Favored  : 74.81 %
  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:  2.10 (0.29), residues: 759
  helix:  2.15 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.60 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 531 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.012   0.002   TYR B  51 
 ARG   0.007   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04923 (  690)
  hydrogen bonds       : angle       3.23449 ( 1785)
  covalent geometry    : bond        0.00418 (11895)
  covalent geometry    : angle       0.62008 (17116)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9972.63 seconds
wall clock time: 173 minutes 19.10 seconds (10399.10 seconds total)