Starting phenix.real_space_refine
on Wed Feb  4 10:05:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d3m_46538/02_2026/9d3m_46538.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.051
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     202      5.49       5
     S      14      5.16       5
     C    5768      2.51       5
     N    1939      2.21       5
     O    2280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10203
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "I"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2079
          Classifications: {'DNA': 101}
          Link IDs: {'rna3p': 100}
    Chain: "J"
      Number of atoms: 2062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2062
          Classifications: {'DNA': 101}
          Link IDs: {'rna3p': 100}
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 788
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 783
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 730
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "K"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Classifications: {'peptide': 5}
          Link IDs: {'TRANS': 4}
    Chain: "L"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 52
          Classifications: {'peptide': 6}
          Link IDs: {'TRANS': 5}
  Time building chain proxies: 2.43, per 1000 atoms: 0.24
  Number of scatterers: 10203
  At special positions: 0
  Unit cell: (90.695, 104.72, 115.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     202     15.00
     O    2280      8.00
     N    1939      7.00
     C    5768      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: 0.80
  Conformation dependent library (CDL) restraints added in 298.5 milliseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1426

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      72.0% alpha, 2.9% beta
      100 base pairs and 178 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.809A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.818A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (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 94
      removed outlier: 3.517A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    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: 4.514A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.683A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.690A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 56
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.510A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    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 73
      removed outlier: 4.446A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.579A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    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 104 through 123
      removed outlier: 3.698A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  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: 6.367A  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: 7.206A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.806A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.970A  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: 7.159A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    407 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      262 hydrogen bonds
      524 hydrogen bond angles
      0 basepair planarities
      100 basepair parallelities
      178 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.12 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: 2138
        1.33 -     1.45: 3112
        1.45 -     1.57: 5106
        1.57 -     1.69: 402
        1.69 -     1.81: 26
  Bond restraints: 10784
  Sorted by residual:
  bond pdb=" CB  ASN G  73 "
       pdb=" CG  ASN G  73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.555 -0.039 2.50e-02 1.60e+03 2.48e+00
  bond pdb=" CA  ASN G  73 "
       pdb=" C   ASN G  73 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.025 1.59e-02 3.96e+03 2.41e+00
  bond pdb=" CA  ASN G  73 "
       pdb=" CB  ASN G  73 "
    ideal  model  delta    sigma   weight residual
    1.529  1.547 -0.018 1.34e-02 5.57e+03 1.86e+00
  bond pdb=" C4'  DT I  18 "
       pdb=" C3'  DT I  18 "
    ideal  model  delta    sigma   weight residual
    1.523  1.501  0.022 2.00e-02 2.50e+03 1.19e+00
  bond pdb=" CB  LYS B  44 "
       pdb=" CG  LYS B  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.18e+00
  ... (remaining 10779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 14544
        1.04 -     2.08: 672
        2.08 -     3.13: 166
        3.13 -     4.17: 17
        4.17 -     5.21: 10
  Bond angle restraints: 15409
  Sorted by residual:
  angle pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" C   ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.97  108.90    4.07 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
        pdb=" CG  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.60  116.26   -3.66 1.00e+00 1.00e+00 1.34e+01
  angle pdb=" C   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     111.17  115.95   -4.78 1.53e+00 4.27e-01 9.76e+00
  angle pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     110.65  106.99    3.66 1.42e+00 4.96e-01 6.64e+00
  angle pdb=" CA  LYS D 108 "
        pdb=" CB  LYS D 108 "
        pdb=" CG  LYS D 108 "
      ideal   model   delta    sigma   weight residual
     114.10  118.28   -4.18 2.00e+00 2.50e-01 4.37e+00
  ... (remaining 15404 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 4890
       35.44 -    70.87: 1074
       70.87 -   106.31: 13
      106.31 -   141.74: 0
      141.74 -   177.18: 2
  Dihedral angle restraints: 5979
    sinusoidal: 3768
      harmonic: 2211
  Sorted by residual:
  dihedral pdb=" C4'  DA J -16 "
           pdb=" C3'  DA J -16 "
           pdb=" O3'  DA J -16 "
           pdb=" P    DG J -15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.18 -177.18     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  21 "
           pdb=" C3'  DG J  21 "
           pdb=" O3'  DG J  21 "
           pdb=" P    DG J  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.44  142.56     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" CG  ARG A 116 "
           pdb=" CD  ARG A 116 "
           pdb=" NE  ARG A 116 "
           pdb=" CZ  ARG A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.06   43.06     2      1.50e+01 4.44e-03 9.95e+00
  ... (remaining 5976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1166
       0.031 -    0.063: 464
       0.063 -    0.094: 83
       0.094 -    0.125: 35
       0.125 -    0.157: 4
  Chirality restraints: 1752
  Sorted by residual:
  chirality pdb=" CG  LEU A  48 "
            pdb=" CB  LEU A  48 "
            pdb=" CD1 LEU A  48 "
            pdb=" CD2 LEU A  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  ILE C 102 "
            pdb=" N   ILE C 102 "
            pdb=" C   ILE C 102 "
            pdb=" CB  ILE C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  VAL F  21 "
            pdb=" N   VAL F  21 "
            pdb=" C   VAL F  21 "
            pdb=" CB  VAL F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1749 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO G  80 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  -2 "   -0.019 2.00e-02 2.50e+03   8.68e-03 2.07e+00
        pdb=" N9   DA I  -2 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I  -2 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I  -2 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  -2 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  -2 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  -2 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  -2 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  -2 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DA I  -2 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DA I  -2 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  28 "    0.019 2.00e-02 2.50e+03   9.22e-03 1.91e+00
        pdb=" N1   DC I  28 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DC I  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DC I  28 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  28 "    0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  28 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DC I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC I  28 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 258
        2.67 -     3.23: 8681
        3.23 -     3.78: 18255
        3.78 -     4.34: 24623
        4.34 -     4.90: 35721
  Nonbonded interactions: 87538
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OG1 THR B  73 "
            pdb=" OD2 ASP B  85 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE G  78 "
            pdb=" OG  SER H  55 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   SER H 123 "
            pdb=" OG  SER H 123 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASN G  73 "
            pdb=" OD1 ASN G  73 "
     model   vdw
     2.265 3.040
  ... (remaining 87533 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' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = (chain 'C' and (resid 15 through 113 or (resid 114 through 115 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 116 through 117))
  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:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.870
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:5.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10784  Z= 0.200
  Angle     :  0.539   5.210  15409  Z= 0.324
  Chirality :  0.035   0.157   1752
  Planarity :  0.004   0.036   1256
  Dihedral  : 27.356 177.180   4553
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 21.96 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.29), residues: 745
  helix:  1.40 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.74 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  20 
 TYR   0.012   0.002   TYR D  42 
 PHE   0.008   0.002   PHE E 104 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (10784)
  covalent geometry    : angle       0.53920 (15409)
  hydrogen bonds       : bond        0.14670 (  669)
  hydrogen bonds       : angle       4.70283 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.266 
Fit side-chains
REVERT: D   57 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8463 (mmmt)
REVERT: F   84 MET cc_start: 0.8608 (tpp) cc_final: 0.8365 (tpp)
  outliers start: 10
  outliers final: 6
  residues processed: 117
  average time/residue: 0.8283
  time to fit residues: 101.7110
Evaluate side-chains
  112 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.188766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.124637 restraints weight = 11569.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.56
r_work: 0.3311 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10784  Z= 0.152
  Angle     :  0.510   5.100  15409  Z= 0.309
  Chirality :  0.033   0.143   1752
  Planarity :  0.004   0.034   1256
  Dihedral  : 29.394 176.812   3051
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.22 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.30), residues: 745
  helix:  2.55 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.73 (0.38), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  71 
 TYR   0.013   0.001   TYR D  40 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10784)
  covalent geometry    : angle       0.51026 (15409)
  hydrogen bonds       : bond        0.04094 (  669)
  hydrogen bonds       : angle       2.93046 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8748 (tt0) cc_final: 0.8539 (tt0)
REVERT: A  125 GLN cc_start: 0.8814 (mt0) cc_final: 0.8567 (mt0)
REVERT: B   96 THR cc_start: 0.9226 (m) cc_final: 0.8974 (p)
REVERT: C   32 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8167 (ttp80)
REVERT: D   83 TYR cc_start: 0.7640 (m-10) cc_final: 0.7317 (t80)
REVERT: F   84 MET cc_start: 0.8534 (tpp) cc_final: 0.8279 (tpp)
REVERT: F   93 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7110 (mp10)
REVERT: G   73 ASN cc_start: 0.7317 (t0) cc_final: 0.6970 (t0)
REVERT: H   92 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6338 (mtp85)
  outliers start: 17
  outliers final: 4
  residues processed: 119
  average time/residue: 0.8796
  time to fit residues: 109.8910
Evaluate side-chains
  111 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   92 ARG
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 90 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0030
   overall best weight:    2.2596

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C  73 ASN
D  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.186348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121260 restraints weight = 11553.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.60
r_work: 0.3263 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.0960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10784  Z= 0.196
  Angle     :  0.533   5.266  15409  Z= 0.317
  Chirality :  0.035   0.171   1752
  Planarity :  0.004   0.035   1256
  Dihedral  : 29.485 176.656   3047
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.48 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.30), residues: 745
  helix:  2.67 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.94 (0.36), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  71 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.009   0.002   PHE F  61 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10784)
  covalent geometry    : angle       0.53268 (15409)
  hydrogen bonds       : bond        0.04556 (  669)
  hydrogen bonds       : angle       2.99511 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8497 (mtt)
REVERT: C   32 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8140 (ttp80)
REVERT: F   84 MET cc_start: 0.8566 (tpp) cc_final: 0.8266 (tpp)
REVERT: F   93 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7225 (mp10)
REVERT: G   24 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7285 (mm-40)
REVERT: G   32 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7311 (mtm110)
REVERT: G   73 ASN cc_start: 0.7426 (t0) cc_final: 0.6920 (t0)
REVERT: G   77 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7933 (ttm170)
REVERT: H   92 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6395 (mtp85)
REVERT: H   93 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7657 (mp0)
  outliers start: 18
  outliers final: 6
  residues processed: 113
  average time/residue: 0.8389
  time to fit residues: 99.5586
Evaluate side-chains
  113 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue   92 ARG
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 91 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.187301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.122682 restraints weight = 11666.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.56
r_work: 0.3287 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10784  Z= 0.153
  Angle     :  0.511   5.119  15409  Z= 0.309
  Chirality :  0.034   0.145   1752
  Planarity :  0.004   0.035   1256
  Dihedral  : 29.488 176.882   3046
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.48 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.30), residues: 745
  helix:  2.78 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.95 (0.36), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.008   0.001   PHE F  61 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10784)
  covalent geometry    : angle       0.51141 (15409)
  hydrogen bonds       : bond        0.04236 (  669)
  hydrogen bonds       : angle       2.93211 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.306 
Fit side-chains
REVERT: C   32 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8158 (ttp80)
REVERT: C   74 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7367 (mmtp)
REVERT: D   83 TYR cc_start: 0.7691 (m-10) cc_final: 0.7387 (t80)
REVERT: F   84 MET cc_start: 0.8561 (tpp) cc_final: 0.8271 (tpp)
REVERT: F   93 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7229 (mp10)
REVERT: G   19 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7916 (p)
REVERT: G   24 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7249 (mm-40)
REVERT: G   32 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7320 (mtm110)
REVERT: H   92 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6349 (mtp85)
REVERT: H   93 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7658 (mp0)
  outliers start: 18
  outliers final: 7
  residues processed: 115
  average time/residue: 0.8445
  time to fit residues: 102.0677
Evaluate side-chains
  115 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain H residue   92 ARG
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 3 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   chunk 87 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN
G  89 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.185298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.120362 restraints weight = 11604.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.61
r_work: 0.3250 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10784  Z= 0.211
  Angle     :  0.542   5.441  15409  Z= 0.322
  Chirality :  0.036   0.141   1752
  Planarity :  0.004   0.042   1256
  Dihedral  : 29.576 176.516   3046
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.80 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.30), residues: 745
  helix:  2.61 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.03 (0.36), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.011   0.002   TYR D  40 
 PHE   0.009   0.002   PHE F  61 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (10784)
  covalent geometry    : angle       0.54180 (15409)
  hydrogen bonds       : bond        0.04637 (  669)
  hydrogen bonds       : angle       3.01138 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8528 (mtt)
REVERT: C   32 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8259 (ttp80)
REVERT: C   35 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6288 (mtt90)
REVERT: C   74 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7362 (mmtp)
REVERT: F   84 MET cc_start: 0.8608 (tpp) cc_final: 0.8364 (tpp)
REVERT: G   19 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7884 (p)
REVERT: G   73 ASN cc_start: 0.7595 (t0) cc_final: 0.7032 (t0)
REVERT: H   92 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6520 (mtp85)
  outliers start: 21
  outliers final: 9
  residues processed: 113
  average time/residue: 0.9466
  time to fit residues: 111.8363
Evaluate side-chains
  115 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue   92 ARG
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 60 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.187178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122800 restraints weight = 11719.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.57
r_work: 0.3289 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10784  Z= 0.144
  Angle     :  0.514   5.152  15409  Z= 0.310
  Chirality :  0.034   0.143   1752
  Planarity :  0.004   0.042   1256
  Dihedral  : 29.571 176.920   3046
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 22.59 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.30), residues: 745
  helix:  2.71 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.88 (0.38), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  71 
 TYR   0.010   0.001   TYR H  40 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10784)
  covalent geometry    : angle       0.51441 (15409)
  hydrogen bonds       : bond        0.04159 (  669)
  hydrogen bonds       : angle       2.90792 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.217 
Fit side-chains
REVERT: C   32 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8138 (ttp80)
REVERT: C   35 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6258 (mtt90)
REVERT: C   74 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7339 (mmtp)
REVERT: D   83 TYR cc_start: 0.7695 (m-10) cc_final: 0.7376 (t80)
REVERT: F   84 MET cc_start: 0.8555 (tpp) cc_final: 0.8301 (tpp)
REVERT: G   19 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7870 (p)
REVERT: G   32 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7315 (mtm110)
REVERT: G   73 ASN cc_start: 0.7563 (t0) cc_final: 0.6962 (t0)
REVERT: H   93 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7616 (mp0)
  outliers start: 19
  outliers final: 8
  residues processed: 116
  average time/residue: 0.7876
  time to fit residues: 95.8749
Evaluate side-chains
  114 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   36 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.186281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121549 restraints weight = 11579.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.60
r_work: 0.3273 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10784  Z= 0.181
  Angle     :  0.522   6.081  15409  Z= 0.312
  Chirality :  0.035   0.190   1752
  Planarity :  0.004   0.039   1256
  Dihedral  : 29.485 176.599   3046
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 23.22 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.30), residues: 745
  helix:  2.74 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.90 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.010   0.001   TYR H  40 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (10784)
  covalent geometry    : angle       0.52238 (15409)
  hydrogen bonds       : bond        0.04273 (  669)
  hydrogen bonds       : angle       2.90960 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.280 
Fit side-chains
REVERT: C   32 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8109 (ttp80)
REVERT: C   35 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6260 (mtt90)
REVERT: C   74 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7351 (mmtp)
REVERT: D   83 TYR cc_start: 0.7722 (m-10) cc_final: 0.7378 (t80)
REVERT: F   84 MET cc_start: 0.8573 (tpp) cc_final: 0.8314 (tpp)
REVERT: G   19 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7877 (p)
REVERT: G   24 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7242 (mm-40)
REVERT: G   73 ASN cc_start: 0.7576 (t0) cc_final: 0.6952 (t0)
REVERT: H   93 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7678 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 0.8219
  time to fit residues: 93.0532
Evaluate side-chains
  111 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.185839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121105 restraints weight = 11583.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.61
r_work: 0.3270 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10784  Z= 0.191
  Angle     :  0.530   5.219  15409  Z= 0.315
  Chirality :  0.035   0.179   1752
  Planarity :  0.004   0.036   1256
  Dihedral  : 29.501 176.802   3046
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.91 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.30), residues: 745
  helix:  2.62 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.85 (0.38), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  71 
 TYR   0.010   0.001   TYR H  40 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (10784)
  covalent geometry    : angle       0.52982 (15409)
  hydrogen bonds       : bond        0.04393 (  669)
  hydrogen bonds       : angle       2.93439 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: C   32 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8161 (ttp80)
REVERT: C   35 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6260 (mtt90)
REVERT: C   74 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7374 (mmtp)
REVERT: D   83 TYR cc_start: 0.7742 (m-10) cc_final: 0.7343 (t80)
REVERT: D   86 ARG cc_start: 0.7537 (mmt90) cc_final: 0.7325 (mtt90)
REVERT: F   84 MET cc_start: 0.8572 (tpp) cc_final: 0.8249 (tpp)
REVERT: G   19 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7858 (p)
REVERT: G   24 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7276 (mm-40)
REVERT: G   32 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7455 (mtm110)
REVERT: G   73 ASN cc_start: 0.7514 (t0) cc_final: 0.6895 (t0)
REVERT: G   77 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7890 (ttm170)
REVERT: H   93 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7664 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 110
  average time/residue: 0.8959
  time to fit residues: 103.3695
Evaluate side-chains
  113 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 73 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0770
   chunk 86 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.187445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.122957 restraints weight = 11580.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.58
r_work: 0.3290 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10784  Z= 0.141
  Angle     :  0.516   5.118  15409  Z= 0.310
  Chirality :  0.034   0.212   1752
  Planarity :  0.004   0.043   1256
  Dihedral  : 29.507 177.114   3046
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 23.22 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.30), residues: 745
  helix:  2.80 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.89 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.011   0.001   TYR G  57 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10784)
  covalent geometry    : angle       0.51580 (15409)
  hydrogen bonds       : bond        0.04069 (  669)
  hydrogen bonds       : angle       2.87414 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.226 
Fit side-chains
REVERT: C   32 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8100 (ttp80)
REVERT: C   35 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6257 (mtt90)
REVERT: C   74 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7379 (mmtp)
REVERT: D   83 TYR cc_start: 0.7705 (m-10) cc_final: 0.7343 (t80)
REVERT: D   86 ARG cc_start: 0.7538 (mmt90) cc_final: 0.7334 (mtt90)
REVERT: F   84 MET cc_start: 0.8541 (tpp) cc_final: 0.8286 (tpp)
REVERT: G   19 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7850 (p)
REVERT: G   32 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7450 (mtm110)
REVERT: G   73 ASN cc_start: 0.7560 (t0) cc_final: 0.6962 (t0)
REVERT: H   93 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7600 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 109
  average time/residue: 0.7773
  time to fit residues: 88.9131
Evaluate side-chains
  111 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0670
   overall best weight:    1.9524

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.186494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122280 restraints weight = 11481.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.56
r_work: 0.3281 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10784  Z= 0.180
  Angle     :  0.523   5.162  15409  Z= 0.312
  Chirality :  0.035   0.163   1752
  Planarity :  0.004   0.040   1256
  Dihedral  : 29.457 176.646   3046
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 23.06 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.30), residues: 745
  helix:  2.76 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.89 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  71 
 TYR   0.011   0.002   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10784)
  covalent geometry    : angle       0.52252 (15409)
  hydrogen bonds       : bond        0.04272 (  669)
  hydrogen bonds       : angle       2.89827 ( 1727)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.251 
Fit side-chains
REVERT: C   32 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8126 (ttp80)
REVERT: C   35 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6281 (mtt90)
REVERT: C   74 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7361 (mmtp)
REVERT: D   83 TYR cc_start: 0.7737 (m-10) cc_final: 0.7379 (t80)
REVERT: D   86 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7327 (mtt90)
REVERT: F   84 MET cc_start: 0.8561 (tpp) cc_final: 0.8305 (tpp)
REVERT: G   19 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7825 (p)
REVERT: G   32 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7357 (mtm110)
REVERT: G   73 ASN cc_start: 0.7574 (t0) cc_final: 0.6975 (t0)
REVERT: H   93 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7681 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 108
  average time/residue: 0.7970
  time to fit residues: 90.2936
Evaluate side-chains
  110 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   24 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0870
   chunk 59 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.3764

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.185539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121141 restraints weight = 11575.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.57
r_work: 0.3262 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10784  Z= 0.200
  Angle     :  0.539   5.229  15409  Z= 0.319
  Chirality :  0.035   0.165   1752
  Planarity :  0.004   0.043   1256
  Dihedral  : 29.524 176.798   3046
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 23.54 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.30), residues: 745
  helix:  2.63 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.92 (0.37), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  71 
 TYR   0.012   0.002   TYR G  57 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (10784)
  covalent geometry    : angle       0.53867 (15409)
  hydrogen bonds       : bond        0.04505 (  669)
  hydrogen bonds       : angle       2.96004 ( 1727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3888.75 seconds
wall clock time: 66 minutes 42.09 seconds (4002.09 seconds total)