Starting phenix.real_space_refine
on Fri Sep 11 06:00:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lv9_23530/09_2026/7lv9_23530.map"
  }
  resolution = 4.5
  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=  -0.000 sd=   1.006
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     190      5.49       5
     S      26      5.16       5
     C    4566      2.51       5
     N    1515      2.21       5
     O    1941      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8238
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 731
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "A"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 772
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 659
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 680
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 93}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 731
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 770
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 1931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1931
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
    Chain: "H"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1964
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
  Time building chain proxies: 1.69, per 1000 atoms: 0.21
  Number of scatterers: 8238
  At special positions: 0
  Unit cell: (71.94, 115.54, 118.81, 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      26     16.00
     P     190     15.00
     O    1941      8.00
     N    1515      7.00
     C    4566      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
  Links applied
    TRANS
      " CYS A 113 " - " SER B 112 "
      " GLU C 105 " - " LYS D 104 "
      " CYS E 113 " - " SER F 112 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 186.0 milliseconds
  

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1074

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      64.7% alpha, 1.7% beta
      88 base pairs and 161 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 40
      removed outlier: 3.570A  pdb=" N   GLN B  33 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 74
      removed outlier: 3.594A  pdb=" N   LEU B  69 " --> pdb=" O   GLN B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 89
      removed outlier: 3.545A  pdb=" N   VAL B  84 " --> pdb=" O   MET B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 92
      No H-bonds generated for 'chain 'B' and resid 90 through 92'
    Processing helix  chain 'A' and resid 127 through 136
      removed outlier: 3.525A  pdb=" N   VAL A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 160
      removed outlier: 3.848A  pdb=" N   GLU A 159 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 195
      removed outlier: 3.586A  pdb=" N   ILE A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 211
      removed outlier: 3.717A  pdb=" N   ILE A 205 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 29
    Processing helix  chain 'D' and resid 35 through 61
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 3.698A  pdb=" N   VAL D  73 " --> pdb=" O   LYS D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 103
      removed outlier: 3.547A  pdb=" N   GLY D  91 " --> pdb=" O   ARG D  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 138 through 167
      removed outlier: 3.771A  pdb=" N   ALA C 142 " --> pdb=" O   SER C 138 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL C 143 " --> pdb=" O   GLU C 139 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 183
      removed outlier: 3.546A  pdb=" N   ILE C 181 " --> pdb=" O   ILE C 177 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN C 182 " --> pdb=" O   THR C 178 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 189
      removed outlier: 3.734A  pdb=" N   ALA C 189 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 28 through 39
      removed outlier: 3.660A  pdb=" N   LEU F  36 " --> pdb=" O   THR F  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 74
      removed outlier: 3.675A  pdb=" N   LEU F  69 " --> pdb=" O   GLN F  65 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA F  74 " --> pdb=" O   ALA F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 91
      removed outlier: 3.554A  pdb=" N   VAL F  84 " --> pdb=" O   MET F  80 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET F  91 " --> pdb=" O   ALA F  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 136
      removed outlier: 3.511A  pdb=" N   VAL E 132 " --> pdb=" O   ASN E 128 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 158
      removed outlier: 3.740A  pdb=" N   LYS E 158 " --> pdb=" O   GLU E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 195
      removed outlier: 3.502A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 211
      removed outlier: 3.604A  pdb=" N   ILE E 205 " --> pdb=" O   THR E 201 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44
      removed outlier: 6.959A  pdb=" N   SER B  43 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 78 through 79
    Processing sheet with id=AA3, first strand: chain 'D' and resid 33 through 34
      removed outlier: 7.202A  pdb=" N   SER D  33 " --> pdb=" O   ILE C 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 67 through 68
    Processing sheet with id=AA5, first strand: chain 'F' and resid 78 through 79

    255 hydrogen bonds defined for protein.
    765 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      228 hydrogen bonds
      456 hydrogen bond angles
      0 basepair planarities
      88 basepair parallelities
      161 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1568
        1.33 -     1.45: 2740
        1.45 -     1.57: 4025
        1.57 -     1.69: 378
        1.69 -     1.81: 45
  Bond restraints: 8756
  Sorted by residual:
  bond pdb=" C3'  DG H  20 "
       pdb=" O3'  DG H  20 "
    ideal  model  delta    sigma   weight residual
    1.435  1.485 -0.050 1.30e-02 5.92e+03 1.48e+01
  bond pdb=" C5'  DA G  57 "
       pdb=" C4'  DA G  57 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.38e+01
  bond pdb=" C3'  DG H -37 "
       pdb=" C2'  DG H -37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.36e+01
  bond pdb=" C3'  DG H  23 "
       pdb=" C2'  DG H  23 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.21e+01
  bond pdb=" C3'  DC H  11 "
       pdb=" C2'  DC H  11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.18e+01
  ... (remaining 8751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11537
        1.41 -     2.83: 1004
        2.83 -     4.24: 59
        4.24 -     5.66: 13
        5.66 -     7.07: 5
  Bond angle restraints: 12618
  Sorted by residual:
  angle pdb=" O4'  DG G  47 "
        pdb=" C4'  DG G  47 "
        pdb=" C3'  DG G  47 "
      ideal   model   delta    sigma   weight residual
     106.00  102.77    3.23 6.00e-01 2.78e+00 2.90e+01
  angle pdb=" O5'  DA G  57 "
        pdb=" C5'  DA G  57 "
        pdb=" C4'  DA G  57 "
      ideal   model   delta    sigma   weight residual
     109.40  113.09   -3.69 8.00e-01 1.56e+00 2.12e+01
  angle pdb=" N3   DT G -17 "
        pdb=" C4   DT G -17 "
        pdb=" O4   DT G -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.57   -2.67 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" N3   DT G -28 "
        pdb=" C4   DT G -28 "
        pdb=" O4   DT G -28 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  angle pdb=" N3   DT G  12 "
        pdb=" C4   DT G  12 "
        pdb=" O4   DT G  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 12613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.62: 3891
       34.62 -    69.25: 891
       69.25 -   103.87: 13
      103.87 -   138.49: 0
      138.49 -   173.11: 2
  Dihedral angle restraints: 4797
    sinusoidal: 3140
      harmonic: 1657
  Sorted by residual:
  dihedral pdb=" C4'  DG H  20 "
           pdb=" C3'  DG H  20 "
           pdb=" O3'  DG H  20 "
           pdb=" P    DG H  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.89  173.11     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT H -59 "
           pdb=" C3'  DT H -59 "
           pdb=" O3'  DT H -59 "
           pdb=" P    DC H -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.28  143.72     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" N   LYS B  62 "
           pdb=" CA  LYS B  62 "
           pdb=" CB  LYS B  62 "
           pdb=" CG  LYS B  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.61   55.61     3      1.50e+01 4.44e-03 9.36e+00
  ... (remaining 4794 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 900
       0.037 -    0.074: 416
       0.074 -    0.111: 137
       0.111 -    0.148: 9
       0.148 -    0.186: 4
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C3'  DT H -59 "
            pdb=" C4'  DT H -59 "
            pdb=" O3'  DT H -59 "
            pdb=" C2'  DT H -59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" C3'  DG H  20 "
            pdb=" C4'  DG H  20 "
            pdb=" O3'  DG H  20 "
            pdb=" C2'  DG H  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.18 2.00e-01 2.50e+01 8.04e-01
  chirality pdb=" P    DG H  21 "
            pdb=" OP1  DG H  21 "
            pdb=" OP2  DG H  21 "
            pdb=" O5'  DG H  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.51   -0.17 2.00e-01 2.50e+01 7.41e-01
  ... (remaining 1463 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  47 "   -0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ASP B  47 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASP B  47 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   THR B  48 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU E 178 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" CD  GLU E 178 "   -0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU E 178 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU E 178 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC G  36 "   -0.023 2.00e-02 2.50e+03   1.11e-02 2.80e+00
        pdb=" N1   DC G  36 "    0.017 2.00e-02 2.50e+03
        pdb=" C2   DC G  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DC G  36 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DC G  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC G  36 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC G  36 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DC G  36 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DC G  36 "    0.005 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 732
        2.74 -     3.28: 7081
        3.28 -     3.82: 15741
        3.82 -     4.36: 18073
        4.36 -     4.90: 26034
  Nonbonded interactions: 67661
  Sorted by model distance:
  nonbonded pdb=" O   LYS F  29 "
            pdb=" OG1 THR F  32 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG1 THR A 123 "
            pdb=" OP2  DA H -14 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   LEU F  42 "
            pdb=" ND2 ASN E 128 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OE2 GLU D  37 "
            pdb=" OG  SER F 108 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" NZ  LYS B  75 "
            pdb=" OP2  DG H -33 "
     model   vdw
     2.370 3.120
  ... (remaining 67656 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 113 through 122 or (resid 123 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 124 through 214))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.530
  Find NCS groups from input model:        0.060
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8759  Z= 0.538
  Angle     :  0.799   7.072  12627  Z= 0.693
  Chirality :  0.045   0.186   1466
  Planarity :  0.004   0.032    927
  Dihedral  : 27.068 173.114   3714
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.35 (0.25), residues: 569
  helix: -2.29 (0.18), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.76 (0.35), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 129 
 TYR   0.024   0.003   TYR D 100 
 PHE   0.024   0.002   PHE C 152 
 HIS   0.003   0.001   HIS F  57 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00574 /  0.54 ( 8756)
  covalent geometry    : angle       0.79898 /  0.69 (12618)
  hydrogen bonds       : bond        0.20477 / 14.05 (  483)
  hydrogen bonds       : angle       5.61629 /  4.06 ( 1221)
  link_TRANS           : bond        0.00674 /  0.34 (    3)
  link_TRANS           : angle       0.80364 /  0.41 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   24 MET cc_start: 0.8435 (mtp) cc_final: 0.8220 (ttp)
REVERT: E  151 MET cc_start: 0.8408 (mtp) cc_final: 0.7713 (mtt)
REVERT: E  176 ILE cc_start: 0.9069 (mt) cc_final: 0.8435 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0917
  time to fit residues: 8.3459
Evaluate side-chains
  32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   overall best weight:    9.3992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 128 ASN
C 118 GLN
E 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.027792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.021100 restraints weight = 153407.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.021597 restraints weight = 100904.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.021977 restraints weight = 77059.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.022257 restraints weight = 64334.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.022402 restraints weight = 56528.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.123   8759  Z= 0.383
  Angle     :  0.974  10.100  12627  Z= 0.545
  Chirality :  0.050   0.306   1466
  Planarity :  0.008   0.106    927
  Dihedral  : 31.083 177.730   2675
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 23.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.31), residues: 569
  helix:  0.65 (0.25), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.55 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG A 199 
 TYR   0.011   0.003   TYR D  81 
 PHE   0.036   0.004   PHE C 152 
 HIS   0.017   0.003   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00674 /  0.38 ( 8756)
  covalent geometry    : angle       0.97427 /  0.55 (12618)
  hydrogen bonds       : bond        0.12493 /  8.47 (  483)
  hydrogen bonds       : angle       3.87065 /  2.78 ( 1221)
  link_TRANS           : bond        0.00487 /  0.25 (    3)
  link_TRANS           : angle       0.21170 /  0.10 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9689 (tmm) cc_final: 0.9460 (tmm)
REVERT: A  172 MET cc_start: 0.8244 (ptt) cc_final: 0.8024 (ppp)
REVERT: D   93 MET cc_start: 0.9565 (mtm) cc_final: 0.9137 (ptm)
REVERT: C  153 MET cc_start: 0.9208 (mmt) cc_final: 0.8697 (mmm)
REVERT: F   91 MET cc_start: 0.9036 (mmp) cc_final: 0.8804 (mmm)
REVERT: E  151 MET cc_start: 0.9485 (mtp) cc_final: 0.9243 (mtt)
REVERT: E  172 MET cc_start: 0.9791 (tpt) cc_final: 0.9474 (mmm)
REVERT: E  210 MET cc_start: 0.9636 (ttp) cc_final: 0.9312 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0943
  time to fit residues: 5.3341
Evaluate side-chains
  27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 59 optimal weight:   30.0000
   chunk 16 optimal weight:    7.9990
   chunk 55 optimal weight:   50.0000
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:   40.0000
   chunk 52 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 72 optimal weight:   30.0000
   chunk 66 optimal weight:   30.0000
   overall best weight:    6.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 128 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.027091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.020840 restraints weight = 152290.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.021336 restraints weight = 100809.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.021697 restraints weight = 76958.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.021900 restraints weight = 64354.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.022124 restraints weight = 57493.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8759  Z= 0.218
  Angle     :  0.705   7.516  12627  Z= 0.416
  Chirality :  0.045   0.430   1466
  Planarity :  0.005   0.052    927
  Dihedral  : 31.387 179.873   2675
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.74 %
    Favored  : 98.05 %
  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:  1.13 (0.34), residues: 569
  helix:  1.86 (0.26), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.34 (0.37), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  76 
 TYR   0.018   0.002   TYR D  81 
 PHE   0.021   0.002   PHE C 152 
 HIS   0.005   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.22 ( 8756)
  covalent geometry    : angle       0.70537 /  0.42 (12618)
  hydrogen bonds       : bond        0.06840 /  4.72 (  483)
  hydrogen bonds       : angle       3.31956 /  2.32 ( 1221)
  link_TRANS           : bond        0.00145 /  0.07 (    3)
  link_TRANS           : angle       0.15836 /  0.09 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9751 (tmm) cc_final: 0.9527 (tmm)
REVERT: B   71 MET cc_start: 0.8914 (tmm) cc_final: 0.8571 (tmm)
REVERT: B   80 MET cc_start: 0.8899 (mtt) cc_final: 0.8635 (mpp)
REVERT: A  172 MET cc_start: 0.8401 (ptt) cc_final: 0.8034 (ppp)
REVERT: A  173 LEU cc_start: 0.9855 (tp) cc_final: 0.9533 (mt)
REVERT: D   93 MET cc_start: 0.9612 (mtm) cc_final: 0.9199 (ptm)
REVERT: C  153 MET cc_start: 0.9493 (mmt) cc_final: 0.8884 (mmp)
REVERT: F   91 MET cc_start: 0.9110 (mmp) cc_final: 0.8859 (mmm)
REVERT: E  151 MET cc_start: 0.9414 (mtp) cc_final: 0.9104 (mtt)
REVERT: E  172 MET cc_start: 0.9776 (tpt) cc_final: 0.9487 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 35
  average time/residue: 0.0875
  time to fit residues: 4.3930
Evaluate side-chains
  30 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 70 optimal weight:   40.0000
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 56 optimal weight:   40.0000
   chunk 16 optimal weight:    5.9990
   chunk 58 optimal weight:   30.0000
   overall best weight:    1.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  57 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.027754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.021324 restraints weight = 147314.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.021975 restraints weight = 92638.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.022432 restraints weight = 67789.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.022733 restraints weight = 54737.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.022892 restraints weight = 47126.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   8759  Z= 0.149
  Angle     :  0.633  10.010  12627  Z= 0.373
  Chirality :  0.042   0.405   1466
  Planarity :  0.004   0.046    927
  Dihedral  : 31.326 179.701   2675
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.34), residues: 569
  helix:  2.30 (0.27), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.13 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  76 
 TYR   0.016   0.002   TYR D  81 
 PHE   0.018   0.002   PHE C 152 
 HIS   0.002   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.15 ( 8756)
  covalent geometry    : angle       0.63273 /  0.37 (12618)
  hydrogen bonds       : bond        0.05014 /  3.46 (  483)
  hydrogen bonds       : angle       3.08541 /  2.13 ( 1221)
  link_TRANS           : bond        0.00054 /  0.03 (    3)
  link_TRANS           : angle       0.14080 /  0.08 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9749 (tmm) cc_final: 0.9540 (tmm)
REVERT: B   80 MET cc_start: 0.8887 (mtt) cc_final: 0.8548 (mtt)
REVERT: A  172 MET cc_start: 0.8475 (ptt) cc_final: 0.8195 (ppp)
REVERT: A  173 LEU cc_start: 0.9840 (tp) cc_final: 0.9520 (mt)
REVERT: D   24 MET cc_start: 0.9499 (ttm) cc_final: 0.9096 (ttm)
REVERT: C  153 MET cc_start: 0.9404 (mmt) cc_final: 0.8751 (mmp)
REVERT: F   91 MET cc_start: 0.9077 (mmp) cc_final: 0.8818 (mmm)
REVERT: E  151 MET cc_start: 0.9490 (mtp) cc_final: 0.9238 (mtt)
REVERT: E  172 MET cc_start: 0.9758 (tpt) cc_final: 0.9501 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0735
  time to fit residues: 3.5468
Evaluate side-chains
  27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0000
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 55 optimal weight:   50.0000
   chunk 66 optimal weight:   30.0000
   overall best weight:    2.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.027060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.020635 restraints weight = 153982.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.021222 restraints weight = 100739.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.021643 restraints weight = 76437.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.021912 restraints weight = 63152.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.022076 restraints weight = 55314.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8759  Z= 0.152
  Angle     :  0.620   7.753  12627  Z= 0.367
  Chirality :  0.041   0.416   1466
  Planarity :  0.003   0.042    927
  Dihedral  : 31.253 179.156   2675
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.30 %
    Favored  : 98.48 %
  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:  1.99 (0.35), residues: 569
  helix:  2.54 (0.26), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.96 (0.40), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 199 
 TYR   0.015   0.001   TYR D  81 
 PHE   0.016   0.001   PHE C 152 
 HIS   0.005   0.001   HIS F  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.15 ( 8756)
  covalent geometry    : angle       0.61974 /  0.37 (12618)
  hydrogen bonds       : bond        0.05150 /  3.54 (  483)
  hydrogen bonds       : angle       3.04412 /  2.11 ( 1221)
  link_TRANS           : bond        0.00102 /  0.05 (    3)
  link_TRANS           : angle       0.11490 /  0.06 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9746 (tmm) cc_final: 0.9484 (tmm)
REVERT: B   71 MET cc_start: 0.9004 (tmm) cc_final: 0.8696 (tmm)
REVERT: B   80 MET cc_start: 0.8928 (mtt) cc_final: 0.8712 (mpp)
REVERT: A  172 MET cc_start: 0.8518 (ptt) cc_final: 0.8218 (ppp)
REVERT: A  173 LEU cc_start: 0.9856 (tp) cc_final: 0.9559 (mt)
REVERT: D   93 MET cc_start: 0.9580 (mtm) cc_final: 0.9221 (ttp)
REVERT: C  153 MET cc_start: 0.9419 (mmt) cc_final: 0.8768 (mmp)
REVERT: F   91 MET cc_start: 0.9104 (mmp) cc_final: 0.8846 (mmm)
REVERT: E  136 MET cc_start: 0.9558 (ttm) cc_final: 0.9349 (tmm)
REVERT: E  151 MET cc_start: 0.9504 (mtp) cc_final: 0.9260 (mtt)
REVERT: E  172 MET cc_start: 0.9759 (tpt) cc_final: 0.9536 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 33
  average time/residue: 0.0843
  time to fit residues: 4.0606
Evaluate side-chains
  29 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 66 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 11 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  26 GLN
** D  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.024907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2507 r_free = 0.2507 target = 0.018946 restraints weight = 165274.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.019429 restraints weight = 108977.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.019806 restraints weight = 83115.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.019981 restraints weight = 69073.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.020145 restraints weight = 61703.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8759  Z= 0.230
  Angle     :  0.749   8.691  12627  Z= 0.429
  Chirality :  0.045   0.471   1466
  Planarity :  0.006   0.119    927
  Dihedral  : 31.680 173.599   2675
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.29 (0.34), residues: 569
  helix:  1.90 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 199 
 TYR   0.023   0.002   TYR D  81 
 PHE   0.024   0.003   PHE C 152 
 HIS   0.005   0.002   HIS B  57 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.23 ( 8756)
  covalent geometry    : angle       0.74878 /  0.43 (12618)
  hydrogen bonds       : bond        0.09677 /  6.60 (  483)
  hydrogen bonds       : angle       3.50150 /  2.41 ( 1221)
  link_TRANS           : bond        0.00233 /  0.11 (    3)
  link_TRANS           : angle       0.21227 /  0.08 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9747 (tmm) cc_final: 0.9351 (ppp)
REVERT: D   24 MET cc_start: 0.9506 (ttm) cc_final: 0.9130 (ttm)
REVERT: D   93 MET cc_start: 0.9542 (mtm) cc_final: 0.9256 (ptm)
REVERT: C  153 MET cc_start: 0.9467 (mmt) cc_final: 0.8755 (mmp)
REVERT: F   91 MET cc_start: 0.9146 (mmp) cc_final: 0.8912 (mmm)
REVERT: E  171 ASP cc_start: 0.9509 (m-30) cc_final: 0.9200 (m-30)
REVERT: E  172 MET cc_start: 0.9752 (tpt) cc_final: 0.9397 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0854
  time to fit residues: 4.0970
Evaluate side-chains
  27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.024823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.018889 restraints weight = 165345.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.019368 restraints weight = 108514.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.019718 restraints weight = 82505.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.019901 restraints weight = 68732.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.020052 restraints weight = 61547.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.5658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8759  Z= 0.206
  Angle     :  0.697   8.570  12627  Z= 0.403
  Chirality :  0.044   0.453   1466
  Planarity :  0.004   0.059    927
  Dihedral  : 31.912 172.714   2675
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.52 (0.35), residues: 569
  helix:  2.07 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.92 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  76 
 TYR   0.013   0.002   TYR D  81 
 PHE   0.016   0.002   PHE C 152 
 HIS   0.006   0.001   HIS E 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.21 ( 8756)
  covalent geometry    : angle       0.69689 /  0.40 (12618)
  hydrogen bonds       : bond        0.07066 /  4.89 (  483)
  hydrogen bonds       : angle       3.38508 /  2.34 ( 1221)
  link_TRANS           : bond        0.00187 /  0.09 (    3)
  link_TRANS           : angle       0.15075 /  0.08 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9751 (tmm) cc_final: 0.9502 (tmm)
REVERT: A  172 MET cc_start: 0.9203 (ppp) cc_final: 0.8937 (ppp)
REVERT: A  173 LEU cc_start: 0.9802 (mt) cc_final: 0.9543 (mt)
REVERT: D   24 MET cc_start: 0.9431 (ttm) cc_final: 0.9039 (ttm)
REVERT: D   93 MET cc_start: 0.9560 (mtm) cc_final: 0.9236 (ptm)
REVERT: C  153 MET cc_start: 0.9535 (mmt) cc_final: 0.8881 (mmp)
REVERT: F   91 MET cc_start: 0.9145 (mmp) cc_final: 0.8914 (mmm)
REVERT: E  172 MET cc_start: 0.9741 (tpt) cc_final: 0.9530 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0795
  time to fit residues: 3.6545
Evaluate side-chains
  28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 57 optimal weight:   40.0000
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 65 optimal weight:   40.0000
   chunk 66 optimal weight:   30.0000
   overall best weight:    5.1188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 174 GLN
E 164 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.024240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.018251 restraints weight = 161365.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.018698 restraints weight = 104267.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.019052 restraints weight = 78894.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.019301 restraints weight = 65532.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.019467 restraints weight = 57772.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.6163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8759  Z= 0.202
  Angle     :  0.703   8.284  12627  Z= 0.403
  Chirality :  0.044   0.439   1466
  Planarity :  0.005   0.055    927
  Dihedral  : 32.087 172.241   2675
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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:  1.42 (0.34), residues: 569
  helix:  2.01 (0.26), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.03 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 133 
 TYR   0.011   0.001   TYR D  81 
 PHE   0.016   0.002   PHE C 152 
 HIS   0.003   0.001   HIS B  57 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.20 ( 8756)
  covalent geometry    : angle       0.70359 /  0.40 (12618)
  hydrogen bonds       : bond        0.06934 /  4.80 (  483)
  hydrogen bonds       : angle       3.40136 /  2.35 ( 1221)
  link_TRANS           : bond        0.00194 /  0.09 (    3)
  link_TRANS           : angle       0.16536 /  0.08 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 MET cc_start: 0.9709 (tmm) cc_final: 0.9509 (tmm)
REVERT: A  172 MET cc_start: 0.9177 (ppp) cc_final: 0.8842 (ppp)
REVERT: A  173 LEU cc_start: 0.9784 (mt) cc_final: 0.9469 (mt)
REVERT: D   24 MET cc_start: 0.9479 (ttm) cc_final: 0.9271 (ptm)
REVERT: D   93 MET cc_start: 0.9549 (mtm) cc_final: 0.9189 (ptm)
REVERT: C  153 MET cc_start: 0.9507 (mmt) cc_final: 0.8799 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0857
  time to fit residues: 4.0038
Evaluate side-chains
  28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 60 optimal weight:   30.0000
   chunk 47 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 72 optimal weight:   40.0000
   chunk 46 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 61 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   overall best weight:    5.7988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.023750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2462 r_free = 0.2462 target = 0.017859 restraints weight = 162648.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.018301 restraints weight = 104414.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2492 r_free = 0.2492 target = 0.018635 restraints weight = 79359.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2501 r_free = 0.2501 target = 0.018860 restraints weight = 66308.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2507 r_free = 0.2507 target = 0.019006 restraints weight = 58838.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.6567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8759  Z= 0.218
  Angle     :  0.718   8.521  12627  Z= 0.413
  Chirality :  0.045   0.441   1466
  Planarity :  0.004   0.049    927
  Dihedral  : 32.230 171.935   2675
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.23 (0.34), residues: 569
  helix:  1.79 (0.25), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.94 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  76 
 TYR   0.009   0.002   TYR D 100 
 PHE   0.015   0.002   PHE C 152 
 HIS   0.003   0.001   HIS F  19 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.22 ( 8756)
  covalent geometry    : angle       0.71814 /  0.41 (12618)
  hydrogen bonds       : bond        0.07620 /  5.27 (  483)
  hydrogen bonds       : angle       3.47009 /  2.41 ( 1221)
  link_TRANS           : bond        0.00213 /  0.10 (    3)
  link_TRANS           : angle       0.27378 /  0.15 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 MET cc_start: 0.9157 (ppp) cc_final: 0.8870 (ppp)
REVERT: A  173 LEU cc_start: 0.9781 (mt) cc_final: 0.9558 (mt)
REVERT: D   24 MET cc_start: 0.9420 (ttm) cc_final: 0.9081 (ttm)
REVERT: D   93 MET cc_start: 0.9558 (mtm) cc_final: 0.9232 (ptm)
REVERT: C  153 MET cc_start: 0.9522 (mmt) cc_final: 0.8841 (mmp)
REVERT: F   91 MET cc_start: 0.9067 (mmp) cc_final: 0.8838 (mmm)
REVERT: E  151 MET cc_start: 0.9495 (mtt) cc_final: 0.8964 (mmt)
REVERT: E  172 MET cc_start: 0.9404 (mmt) cc_final: 0.8898 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0758
  time to fit residues: 3.3658
Evaluate side-chains
  27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:    0.1980
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0770
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 68 optimal weight:   30.0000
   chunk 61 optimal weight:   30.0000
   overall best weight:    2.2544

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  26 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.024239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2476 r_free = 0.2476 target = 0.018155 restraints weight = 156716.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2495 r_free = 0.2495 target = 0.018689 restraints weight = 101337.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2511 r_free = 0.2511 target = 0.019062 restraints weight = 76223.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.019312 restraints weight = 63108.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.019403 restraints weight = 55639.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.6508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8759  Z= 0.144
  Angle     :  0.654   7.322  12627  Z= 0.379
  Chirality :  0.044   0.425   1466
  Planarity :  0.003   0.031    927
  Dihedral  : 32.138 172.627   2675
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.78 (0.35), residues: 569
  helix:  2.30 (0.26), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.92 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 111 
 TYR   0.008   0.001   TYR D  81 
 PHE   0.012   0.001   PHE C 152 
 HIS   0.003   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.14 ( 8756)
  covalent geometry    : angle       0.65381 /  0.38 (12618)
  hydrogen bonds       : bond        0.04894 /  3.41 (  483)
  hydrogen bonds       : angle       3.16351 /  2.19 ( 1221)
  link_TRANS           : bond        0.00066 /  0.03 (    3)
  link_TRANS           : angle       0.28444 /  0.15 (    9)

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 MET cc_start: 0.9105 (ppp) cc_final: 0.8810 (ppp)
REVERT: A  173 LEU cc_start: 0.9783 (mt) cc_final: 0.9543 (mt)
REVERT: D   24 MET cc_start: 0.9442 (ttm) cc_final: 0.9114 (ttm)
REVERT: D   93 MET cc_start: 0.9574 (mtm) cc_final: 0.9155 (ptm)
REVERT: C  153 MET cc_start: 0.9490 (mmt) cc_final: 0.8839 (mmp)
REVERT: F   91 MET cc_start: 0.9063 (mmp) cc_final: 0.8819 (mmm)
REVERT: E  151 MET cc_start: 0.9515 (mtt) cc_final: 0.9084 (mmt)
REVERT: E  171 ASP cc_start: 0.9487 (m-30) cc_final: 0.9250 (m-30)
REVERT: E  172 MET cc_start: 0.9461 (mmt) cc_final: 0.8869 (mmm)
REVERT: E  210 MET cc_start: 0.8539 (tpt) cc_final: 0.8204 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0652
  time to fit residues: 3.2656
Evaluate side-chains
  28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:   30.0000
   chunk 49 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0370
   chunk 64 optimal weight:   40.0000
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 68 optimal weight:   30.0000
   chunk 33 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    4.4066

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.023715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.017821 restraints weight = 159531.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2476 r_free = 0.2476 target = 0.018300 restraints weight = 102926.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.018495 restraints weight = 78302.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2498 r_free = 0.2498 target = 0.018824 restraints weight = 68189.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2504 r_free = 0.2504 target = 0.018942 restraints weight = 59396.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.6899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8759  Z= 0.182
  Angle     :  0.672   8.355  12627  Z= 0.389
  Chirality :  0.043   0.406   1466
  Planarity :  0.004   0.040    927
  Dihedral  : 32.123 173.234   2675
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  1.70 (0.35), residues: 569
  helix:  2.27 (0.26), residues: 363
  sheet:  None (None), residues: 0
  loop : -1.02 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 111 
 TYR   0.008   0.001   TYR D 100 
 PHE   0.014   0.002   PHE C 152 
 HIS   0.004   0.001   HIS F  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.18 ( 8756)
  covalent geometry    : angle       0.67267 /  0.39 (12618)
  hydrogen bonds       : bond        0.06899 /  4.72 (  483)
  hydrogen bonds       : angle       3.24923 /  2.25 ( 1221)
  link_TRANS           : bond        0.00164 /  0.08 (    3)
  link_TRANS           : angle       0.26718 /  0.15 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1095.31 seconds
wall clock time: 19 minutes 43.24 seconds (1183.24 seconds total)