Starting phenix.real_space_refine
on Thu Mar  5 06:33:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xcr_33126/03_2026/7xcr_33126.map"
  }
  resolution = 2.57
  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=  -0.001 sd=   0.114
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic.
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     292      5.49       5
     S      26      5.16       5
     C    8789      2.51       5
     N    2847      2.21       5
     O    3446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15400
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "L"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 707
          Classifications: {'peptide': 88}
          Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "K"
      Number of atoms: 2671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2671
          Classifications: {'peptide': 328}
          Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU L  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU L  73 " occ=0.45
    residue:
      pdb=" N   ARG L  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  74 " occ=0.45
    residue:
      pdb=" N   GLY L  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY L  75 " occ=0.25
    residue:
      pdb=" N   GLY L  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY L  76 " occ=0.25
  Time building chain proxies: 3.16, per 1000 atoms: 0.21
  Number of scatterers: 15400
  At special positions: 0
  Unit cell: (120.96, 122.04, 130.68, 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     292     15.00
     O    3446      8.00
     N    2847      7.00
     C    8789      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: 1.40
  Conformation dependent library (CDL) restraints added in 442.5 milliseconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2206

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      55.7% alpha, 5.5% beta
      135 base pairs and 277 stacking pairs defined.
    Time for finding SS restraints: 2.47
  Creating SS restraints...
    Processing helix  chain 'L' and resid 22 through 34
      removed outlier: 4.048A  pdb=" N   GLN L  31 " --> pdb=" O   LYS L  27 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 37 through 41
      removed outlier: 4.040A  pdb=" N   GLN L  41 " --> pdb=" O   PRO L  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 35
    Processing helix  chain 'F' and resid 49 through 57
      removed outlier: 3.598A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.524A  pdb=" N   ILE G  62 " --> pdb=" O   LEU G  58 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.699A  pdb=" N   LYS H  46 " --> pdb=" O   TYR H  42 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.616A  pdb=" N   ILE H  61 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 122
      removed outlier: 3.501A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 34 through 46
      removed outlier: 4.028A  pdb=" N   ARG K  42 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP K  43 " --> pdb=" O   GLU K  39 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU K  46 " --> pdb=" O   ARG K  42 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 50 through 55
    Processing helix  chain 'K' and resid 67 through 81
      removed outlier: 4.338A  pdb=" N   MET K  71 " --> pdb=" O   SER K  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU K  74 " --> pdb=" O   SER K  70 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASP K  76 " --> pdb=" O   GLN K  72 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LYS K  77 " --> pdb=" O   ARG K  73 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 82 through 87
      removed outlier: 3.596A  pdb=" N   GLN K  87 " --> pdb=" O   ASP K  83 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 88 through 90
      No H-bonds generated for 'chain 'K' and resid 88 through 90'
    Processing helix  chain 'K' and resid 103 through 119
    Processing helix  chain 'K' and resid 121 through 127
    Processing helix  chain 'K' and resid 140 through 151
      removed outlier: 3.553A  pdb=" N   VAL K 144 " --> pdb=" O   SER K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 175
      removed outlier: 3.556A  pdb=" N   LEU K 171 " --> pdb=" O   GLY K 167 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN K 172 " --> pdb=" O   GLN K 168 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 188 through 208
      removed outlier: 3.709A  pdb=" N   THR K 197 " --> pdb=" O   LYS K 193 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG K 203 " --> pdb=" O   ASP K 199 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 225 through 234
      removed outlier: 3.524A  pdb=" N   ARG K 229 " --> pdb=" O   SER K 225 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLU K 230 " --> pdb=" O   GLU K 226 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG K 231 " --> pdb=" O   GLU K 227 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA K 233 " --> pdb=" O   ARG K 229 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 258
      removed outlier: 3.506A  pdb=" N   GLN K 252 " --> pdb=" O   GLU K 248 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU K 255 " --> pdb=" O   HIS K 251 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 286 through 289
      removed outlier: 3.521A  pdb=" N   THR K 289 " --> pdb=" O   ASP K 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 286 through 289'
    Processing helix  chain 'K' and resid 321 through 327
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 75
      removed outlier: 3.514A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 79
      removed outlier: 3.557A  pdb=" N   NLE E  79 " --> pdb=" O   GLN E  76 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 76 through 79'
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.572A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.595A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.564A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.621A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.575A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.524A  pdb=" N   ILE C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.728A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.515A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 16
      removed outlier: 3.624A  pdb=" N   PHE L  45 " --> pdb=" O   LYS L  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46
      removed outlier: 7.199A  pdb=" N   ARG F  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.155A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.062A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102
      removed outlier: 6.758A  pdb=" N   THR G 101 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7
    Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220
      removed outlier: 6.479A  pdb=" N   HIS K 182 " --> pdb=" O   THR K 217 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   GLU K 219 " --> pdb=" O   HIS K 182 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLY K 184 " --> pdb=" O   GLU K 219 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   PHE K 159 " --> pdb=" O   HIS K 181 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE K 238 " --> pdb=" O   VAL K 267 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.235A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'D' and resid 88 through 89

    449 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      338 hydrogen bonds
      668 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      277 stacking parallelities
  Total time for adding SS restraints: 3.12

  Time building geometry restraints manager: 1.77 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: 2831
        1.33 -     1.45: 5088
        1.45 -     1.57: 7738
        1.57 -     1.69: 582
        1.69 -     1.81: 48
  Bond restraints: 16287
  Sorted by residual:
  bond pdb=" C   ALA F  69 "
       pdb=" N   VAL F  70 "
    ideal  model  delta    sigma   weight residual
    1.335  1.298  0.036 1.16e-02 7.43e+03 9.90e+00
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.64e+00
  bond pdb=" C2  SAM K 500 "
       pdb=" N3  SAM K 500 "
    ideal  model  delta    sigma   weight residual
    1.322  1.373 -0.051 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" C2  SAM K 500 "
       pdb=" N1  SAM K 500 "
    ideal  model  delta    sigma   weight residual
    1.329  1.378 -0.049 2.00e-02 2.50e+03 6.01e+00
  bond pdb=" C8  SAM K 500 "
       pdb=" N7  SAM K 500 "
    ideal  model  delta    sigma   weight residual
    1.298  1.346 -0.048 2.00e-02 2.50e+03 5.72e+00
  ... (remaining 16282 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 22986
        3.20 -     6.40: 221
        6.40 -     9.60: 40
        9.60 -    12.79: 5
       12.79 -    15.99: 7
  Bond angle restraints: 23259
  Sorted by residual:
  angle pdb=" C   GLU K  47 "
        pdb=" N   ILE K  48 "
        pdb=" CA  ILE K  48 "
      ideal   model   delta    sigma   weight residual
     121.70  137.69  -15.99 1.80e+00 3.09e-01 7.89e+01
  angle pdb=" N   LEU F  37 "
        pdb=" CA  LEU F  37 "
        pdb=" C   LEU F  37 "
      ideal   model   delta    sigma   weight residual
     114.75  104.75   10.00 1.26e+00 6.30e-01 6.30e+01
  angle pdb=" C   ARG F  67 "
        pdb=" N   ASP F  68 "
        pdb=" CA  ASP F  68 "
      ideal   model   delta    sigma   weight residual
     121.54  134.44  -12.90 1.91e+00 2.74e-01 4.56e+01
  angle pdb=" C   PHE F 100 "
        pdb=" N   GLY F 101 "
        pdb=" CA  GLY F 101 "
      ideal   model   delta    sigma   weight residual
     121.70  133.06  -11.36 1.80e+00 3.09e-01 3.98e+01
  angle pdb=" CA  PHE F 100 "
        pdb=" C   PHE F 100 "
        pdb=" N   GLY F 101 "
      ideal   model   delta    sigma   weight residual
     119.07  125.58   -6.51 1.23e+00 6.61e-01 2.81e+01
  ... (remaining 23254 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 7784
       35.46 -    70.91: 1291
       70.91 -   106.37: 5
      106.37 -   141.83: 1
      141.83 -   177.28: 2
  Dihedral angle restraints: 9083
    sinusoidal: 5667
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" CA  GLN F  27 "
           pdb=" C   GLN F  27 "
           pdb=" N   GLY F  28 "
           pdb=" CA  GLY F  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  116.95   63.05     0      5.00e+00 4.00e-02 1.59e+02
  dihedral pdb=" CA  VAL F  57 "
           pdb=" C   VAL F  57 "
           pdb=" N   LEU F  58 "
           pdb=" CA  LEU F  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.91  -41.09     0      5.00e+00 4.00e-02 6.75e+01
  dihedral pdb=" CA  ASP K  32 "
           pdb=" C   ASP K  32 "
           pdb=" N   ALA K  33 "
           pdb=" CA  ALA K  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.61  -37.39     0      5.00e+00 4.00e-02 5.59e+01
  ... (remaining 9080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 2296
       0.073 -    0.145: 280
       0.145 -    0.218: 43
       0.218 -    0.290: 4
       0.290 -    0.362: 3
  Chirality restraints: 2626
  Sorted by residual:
  chirality pdb=" CB  ILE C  79 "
            pdb=" CA  ILE C  79 "
            pdb=" CG1 ILE C  79 "
            pdb=" CG2 ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CB  ILE G  79 "
            pdb=" CA  ILE G  79 "
            pdb=" CG1 ILE G  79 "
            pdb=" CG2 ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CB  VAL F  43 "
            pdb=" CA  VAL F  43 "
            pdb=" CG1 VAL F  43 "
            pdb=" CG2 VAL F  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  ... (remaining 2623 not shown)

  Planarity restraints: 1940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  57 "   -0.021 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   VAL F  57 "    0.074 2.00e-02 2.50e+03
        pdb=" O   VAL F  57 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   LEU F  58 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  25 "    0.024 2.00e-02 2.50e+03   2.15e-02 8.07e+00
        pdb=" CG  PHE G  25 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  25 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  25 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  25 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  25 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  25 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  25 "   -0.024 2.00e-02 2.50e+03   2.14e-02 8.02e+00
        pdb=" CG  PHE C  25 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  25 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  25 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  25 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  25 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  25 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1937 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2351
        2.76 -     3.30: 12570
        3.30 -     3.83: 28453
        3.83 -     4.37: 36591
        4.37 -     4.90: 52210
  Nonbonded interactions: 132175
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  82 "
            pdb=" O   MET F  84 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR K 154 "
            pdb=" OD1 ASP K 156 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   GLU K  36 "
            pdb=" OG1 THR K  40 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NH2 ARG F  78 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.342 3.120
  ... (remaining 132170 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 135)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 33 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.630
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:7.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
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      :  0.008   0.077  16287  Z= 0.333
  Angle     :  0.969  15.994  23259  Z= 0.543
  Chirality :  0.053   0.362   2626
  Planarity :  0.007   0.069   1940
  Dihedral  : 23.821 177.284   6877
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.27 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  3.40 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.89 %

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: -4.82 (0.18), residues: 1148
  helix: -4.10 (0.09), residues: 665
  sheet: -1.34 (0.51), residues: 80
  loop : -1.44 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B  45 
 TYR   0.031   0.003   TYR K 312 
 PHE   0.049   0.004   PHE G  25 
 TRP   0.040   0.004   TRP K  89 
 HIS   0.015   0.003   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 (16287)
  covalent geometry    : angle       0.96856 (23259)
  hydrogen bonds       : bond        0.29077 (  787)
  hydrogen bonds       : angle       9.89094 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 255
  time to evaluate  : 0.429 
Fit side-chains
REVERT: F   53 GLU cc_start: 0.8494 (tp30) cc_final: 0.8278 (tp30)
REVERT: H   54 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7999 (mt)
REVERT: H   71 GLU cc_start: 0.7217 (pp20) cc_final: 0.6872 (pp20)
REVERT: A   50 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7951 (mt-10)
REVERT: B   52 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7751 (mm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 262
  average time/residue: 1.0084
  time to fit residues: 279.4944
Evaluate side-chains
  174 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 169
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain B residue   97 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
L  60 ASN
F  18 HIS
F  64 ASN
G  24 GLN
G  82 HIS
G  94 ASN
G 110 ASN
H  63 ASN
K  79 ASN
K 146 GLN
K 324 ASN
E  76 GLN
A  39 HIS
A  68 GLN
D  63 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 HIS
C  24 GLN
C  82 HIS
B  25 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.169336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.135281 restraints weight = 17380.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.13
r_work: 0.3501 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3375 r_free = 0.3375    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  16287  Z= 0.207
  Angle     :  0.697  12.934  23259  Z= 0.401
  Chirality :  0.041   0.194   2626
  Planarity :  0.006   0.061   1940
  Dihedral  : 28.796 176.316   4538
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.31 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.51 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.80 %

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: -1.86 (0.22), residues: 1148
  helix: -1.26 (0.17), residues: 674
  sheet: -0.80 (0.56), residues: 82
  loop : -0.92 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  72 
 TYR   0.014   0.001   TYR F  72 
 PHE   0.021   0.002   PHE C  25 
 TRP   0.020   0.003   TRP K  89 
 HIS   0.007   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (16287)
  covalent geometry    : angle       0.69700 (23259)
  hydrogen bonds       : bond        0.05845 (  787)
  hydrogen bonds       : angle       3.51098 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: G   41 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8079 (tt0)
REVERT: G   75 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8623 (mmtm)
REVERT: H   71 GLU cc_start: 0.7834 (pp20) cc_final: 0.7470 (pp20)
REVERT: K  323 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6702 (mp0)
REVERT: A   50 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: D   99 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8348 (mtt180)
REVERT: D  108 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8317 (tttt)
REVERT: C   36 LYS cc_start: 0.8884 (ptmm) cc_final: 0.8673 (mmmt)
REVERT: B   79 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8431 (mppt)
  outliers start: 31
  outliers final: 15
  residues processed: 196
  average time/residue: 0.8613
  time to fit residues: 180.8117
Evaluate side-chains
  176 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  299 LEU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 119 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0980
   chunk 114 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 34 optimal weight:   20.0000
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H  84 ASN
H 109 HIS
D  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.169470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.135632 restraints weight = 17585.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.10
r_work: 0.3496 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16287  Z= 0.198
  Angle     :  0.654  12.689  23259  Z= 0.376
  Chirality :  0.040   0.191   2626
  Planarity :  0.005   0.055   1940
  Dihedral  : 28.752 177.218   4536
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.18 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 11.61 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

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: -0.31 (0.24), residues: 1148
  helix:  0.12 (0.20), residues: 680
  sheet: -0.30 (0.58), residues: 81
  loop : -0.54 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  99 
 TYR   0.016   0.001   TYR F  72 
 PHE   0.016   0.002   PHE K 223 
 TRP   0.019   0.003   TRP K 205 
 HIS   0.005   0.001   HIS K 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (16287)
  covalent geometry    : angle       0.65353 (23259)
  hydrogen bonds       : bond        0.05137 (  787)
  hydrogen bonds       : angle       3.13736 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7880 (mt)
REVERT: H   71 GLU cc_start: 0.7808 (pp20) cc_final: 0.7498 (pp20)
REVERT: K  206 MET cc_start: 0.8360 (mmt) cc_final: 0.7834 (mmt)
REVERT: K  323 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6664 (mp0)
REVERT: A   50 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8265 (mt-10)
REVERT: D   99 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8328 (mtt180)
REVERT: D  108 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8302 (tttt)
REVERT: C   64 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8029 (tm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 192
  average time/residue: 0.8895
  time to fit residues: 182.1709
Evaluate side-chains
  186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  299 LEU
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   chunk 125 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 138 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0770
   overall best weight:    2.6146

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.166886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.132749 restraints weight = 17498.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.11
r_work: 0.3456 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  16287  Z= 0.271
  Angle     :  0.693  12.577  23259  Z= 0.397
  Chirality :  0.043   0.203   2626
  Planarity :  0.005   0.053   1940
  Dihedral  : 28.953 175.565   4536
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.27 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.41 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

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:  0.08 (0.25), residues: 1148
  helix:  0.47 (0.20), residues: 682
  sheet: -0.18 (0.60), residues: 81
  loop : -0.43 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  79 
 TYR   0.012   0.002   TYR F  72 
 PHE   0.017   0.002   PHE G  25 
 TRP   0.025   0.003   TRP K 205 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 (16287)
  covalent geometry    : angle       0.69311 (23259)
  hydrogen bonds       : bond        0.05806 (  787)
  hydrogen bonds       : angle       3.17450 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8013 (mt)
REVERT: A   50 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8393 (mt-10)
REVERT: C   64 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8097 (tm-30)
REVERT: B   78 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8634 (mtp-110)
  outliers start: 31
  outliers final: 23
  residues processed: 187
  average time/residue: 0.9418
  time to fit residues: 187.3704
Evaluate side-chains
  190 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  299 LEU
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   chunk 138 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E  39 HIS
C  24 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.133211 restraints weight = 17510.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.10
r_work: 0.3462 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  16287  Z= 0.253
  Angle     :  0.674  12.549  23259  Z= 0.387
  Chirality :  0.042   0.200   2626
  Planarity :  0.005   0.051   1940
  Dihedral  : 28.959 176.190   4536
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.36 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.71 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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:  0.37 (0.25), residues: 1148
  helix:  0.73 (0.20), residues: 680
  sheet: -0.06 (0.60), residues: 80
  loop : -0.37 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  79 
 TYR   0.012   0.002   TYR D  40 
 PHE   0.015   0.002   PHE K 223 
 TRP   0.027   0.003   TRP K 205 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (16287)
  covalent geometry    : angle       0.67355 (23259)
  hydrogen bonds       : bond        0.05503 (  787)
  hydrogen bonds       : angle       3.10819 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 169
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8041 (mt)
REVERT: H   54 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8515 (tt)
REVERT: H   57 LYS cc_start: 0.9097 (tptt) cc_final: 0.8887 (tptp)
REVERT: K  212 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7600 (mtmt)
REVERT: K  323 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6560 (mp0)
REVERT: A   50 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8409 (mt-10)
REVERT: C   64 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8115 (tm-30)
  outliers start: 38
  outliers final: 25
  residues processed: 192
  average time/residue: 0.8806
  time to fit residues: 180.5740
Evaluate side-chains
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   51 LEU
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  299 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 138 optimal weight:   10.0000
   chunk 115 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E 125 GLN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.166024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131972 restraints weight = 17424.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.11
r_work: 0.3450 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063  16287  Z= 0.285
  Angle     :  0.700  12.517  23259  Z= 0.400
  Chirality :  0.044   0.204   2626
  Planarity :  0.005   0.050   1940
  Dihedral  : 29.077 175.126   4536
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.36 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 13.91 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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:  0.34 (0.25), residues: 1148
  helix:  0.71 (0.20), residues: 689
  sheet: -0.03 (0.61), residues: 80
  loop : -0.44 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  92 
 TYR   0.012   0.002   TYR D  40 
 PHE   0.015   0.002   PHE K 223 
 TRP   0.021   0.003   TRP K 205 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 (16287)
  covalent geometry    : angle       0.70017 (23259)
  hydrogen bonds       : bond        0.05962 (  787)
  hydrogen bonds       : angle       3.16521 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8043 (mt)
REVERT: H   54 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8528 (tt)
REVERT: H   57 LYS cc_start: 0.9109 (tptt) cc_final: 0.8884 (tptp)
REVERT: K  323 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6585 (mp0)
REVERT: K  329 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5658 (tp)
REVERT: A   50 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8371 (mt-10)
REVERT: C   64 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8135 (tm-30)
REVERT: B   78 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8641 (mtp-110)
REVERT: B   95 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7186 (mtp180)
  outliers start: 40
  outliers final: 24
  residues processed: 189
  average time/residue: 0.9041
  time to fit residues: 182.1769
Evaluate side-chains
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  299 LEU
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 31 optimal weight:    0.2980
   chunk 119 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   chunk 126 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
D  67 ASN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.167743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133841 restraints weight = 17288.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 1.07
r_work: 0.3473 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  16287  Z= 0.186
  Angle     :  0.658  12.571  23259  Z= 0.380
  Chirality :  0.040   0.189   2626
  Planarity :  0.005   0.051   1940
  Dihedral  : 29.115 175.774   4536
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.09 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.91 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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:  0.62 (0.25), residues: 1148
  helix:  0.98 (0.20), residues: 686
  sheet:  0.02 (0.61), residues: 80
  loop : -0.38 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  42 
 TYR   0.014   0.001   TYR D  40 
 PHE   0.014   0.001   PHE K 223 
 TRP   0.015   0.002   TRP K 205 
 HIS   0.004   0.001   HIS K 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (16287)
  covalent geometry    : angle       0.65834 (23259)
  hydrogen bonds       : bond        0.05135 (  787)
  hydrogen bonds       : angle       3.07644 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 163
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7995 (mt)
REVERT: H   54 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: H   57 LYS cc_start: 0.9090 (tptt) cc_final: 0.8876 (mptp)
REVERT: K  323 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6651 (mp0)
REVERT: K  329 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5729 (tp)
REVERT: A   50 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8353 (mt-10)
REVERT: C   64 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8093 (tm-30)
REVERT: B   78 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8710 (mtp-110)
REVERT: B   95 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6483 (mmp80)
  outliers start: 38
  outliers final: 22
  residues processed: 187
  average time/residue: 0.8688
  time to fit residues: 173.4494
Evaluate side-chains
  188 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   51 LEU
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   78 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 124 optimal weight:    7.9990
   chunk 105 optimal weight:    0.6980
   chunk 71 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
C  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.168600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.134685 restraints weight = 17490.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.07
r_work: 0.3487 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  16287  Z= 0.174
  Angle     :  0.644  12.626  23259  Z= 0.371
  Chirality :  0.039   0.180   2626
  Planarity :  0.005   0.107   1940
  Dihedral  : 29.043 176.923   4536
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.92 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.01 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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:  0.82 (0.26), residues: 1148
  helix:  1.15 (0.21), residues: 686
  sheet:  0.04 (0.60), residues: 80
  loop : -0.32 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  42 
 TYR   0.013   0.001   TYR D  40 
 PHE   0.014   0.001   PHE K 223 
 TRP   0.014   0.002   TRP K 205 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (16287)
  covalent geometry    : angle       0.64417 (23259)
  hydrogen bonds       : bond        0.04753 (  787)
  hydrogen bonds       : angle       2.99090 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 163
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: F   90 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7999 (mt)
REVERT: H   54 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (tt)
REVERT: K  323 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6686 (mp0)
REVERT: K  329 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5749 (tp)
REVERT: A   50 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8333 (mt-10)
REVERT: D   71 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7943 (mp0)
REVERT: C   64 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8078 (tm-30)
  outliers start: 38
  outliers final: 24
  residues processed: 186
  average time/residue: 0.8573
  time to fit residues: 170.3833
Evaluate side-chains
  186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   51 LEU
Chi-restraints excluded: chain K residue   71 MET
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  155 ASP
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 134 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E 113 HIS
E 125 GLN
D  67 ASN
C  73 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.168011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.133872 restraints weight = 17410.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.06
r_work: 0.3477 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  16287  Z= 0.204
  Angle     :  0.650  13.510  23259  Z= 0.372
  Chirality :  0.040   0.182   2626
  Planarity :  0.005   0.050   1940
  Dihedral  : 28.934 177.185   4536
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.09 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.81 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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:  0.89 (0.26), residues: 1148
  helix:  1.21 (0.21), residues: 686
  sheet:  0.08 (0.60), residues: 80
  loop : -0.29 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  42 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.014   0.001   PHE K 223 
 TRP   0.014   0.002   TRP K 205 
 HIS   0.004   0.001   HIS K 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (16287)
  covalent geometry    : angle       0.64966 (23259)
  hydrogen bonds       : bond        0.04972 (  787)
  hydrogen bonds       : angle       2.96823 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 162
  time to evaluate  : 0.462 
Fit side-chains
REVERT: F   90 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8022 (mt)
REVERT: H   54 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8560 (tt)
REVERT: H   57 LYS cc_start: 0.9135 (tptt) cc_final: 0.8918 (mptp)
REVERT: K   39 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6436 (mm-30)
REVERT: K  323 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6642 (mp0)
REVERT: K  329 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5818 (tp)
REVERT: A   50 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8331 (mt-10)
REVERT: D   71 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7936 (mp0)
REVERT: C   64 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8075 (tm-30)
  outliers start: 33
  outliers final: 23
  residues processed: 181
  average time/residue: 0.8686
  time to fit residues: 168.0236
Evaluate side-chains
  186 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   51 LEU
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 132 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 93 optimal weight:    0.3980
   chunk 44 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E 125 GLN
D  67 ASN
C  73 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.167255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.133372 restraints weight = 17496.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.09
r_work: 0.3464 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16287  Z= 0.236
  Angle     :  0.668  12.640  23259  Z= 0.383
  Chirality :  0.042   0.193   2626
  Planarity :  0.005   0.076   1940
  Dihedral  : 28.990 176.783   4536
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.27 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.91 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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:  0.82 (0.26), residues: 1148
  helix:  1.13 (0.20), residues: 688
  sheet:  0.12 (0.60), residues: 80
  loop : -0.30 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  92 
 TYR   0.011   0.002   TYR D  40 
 PHE   0.014   0.002   PHE K 223 
 TRP   0.016   0.002   TRP K 205 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (16287)
  covalent geometry    : angle       0.66821 (23259)
  hydrogen bonds       : bond        0.05343 (  787)
  hydrogen bonds       : angle       3.01256 ( 1982)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.426 
Fit side-chains
REVERT: F   90 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: G   20 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8233 (ptp-170)
REVERT: H   54 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8516 (tt)
REVERT: H   57 LYS cc_start: 0.9153 (tptt) cc_final: 0.8939 (mptp)
REVERT: K   39 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6465 (mm-30)
REVERT: K  323 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6702 (mp0)
REVERT: A   50 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8353 (mt-10)
REVERT: D   67 ASN cc_start: 0.9052 (m-40) cc_final: 0.8844 (m110)
REVERT: D   71 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7937 (mp0)
REVERT: C   64 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8090 (tm-30)
  outliers start: 31
  outliers final: 24
  residues processed: 182
  average time/residue: 0.8792
  time to fit residues: 170.9987
Evaluate side-chains
  188 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   51 LEU
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  294 VAL
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:   40.0000
   chunk 27 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 105 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H 109 HIS
E 125 GLN
C  73 ASN
B  93 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.168314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.134473 restraints weight = 17328.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.05
r_work: 0.3485 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  16287  Z= 0.165
  Angle     :  0.645  12.709  23259  Z= 0.371
  Chirality :  0.039   0.185   2626
  Planarity :  0.005   0.066   1940
  Dihedral  : 29.025 176.948   4536
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.18 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.62 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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:  0.99 (0.26), residues: 1148
  helix:  1.26 (0.21), residues: 688
  sheet:  0.18 (0.60), residues: 80
  loop : -0.22 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  92 
 TYR   0.015   0.001   TYR D  40 
 PHE   0.012   0.001   PHE K 223 
 TRP   0.016   0.002   TRP K 205 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (16287)
  covalent geometry    : angle       0.64511 (23259)
  hydrogen bonds       : bond        0.04914 (  787)
  hydrogen bonds       : angle       2.98856 ( 1982)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6684.90 seconds
wall clock time: 113 minutes 44.16 seconds (6824.16 seconds total)