Starting phenix.real_space_refine
on Thu Sep 18 15:02:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwi_47249/09_2025/9dwi_47249.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   1.008
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 4192 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     293      5.49       5
     S      19      5.16       5
     C    8313      2.51       5
     N    2722      2.21       5
     O    3314      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14661
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 846
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 733
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 727
    Chain: "E"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 818
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 807
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
      Conformer: "B"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          bond proxies already assigned to first conformer: 738
    Chain: "I"
      Number of atoms: 2383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 2383
          Classifications: {'DNA': 117}
          Link IDs: {'rna3p': 116}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 595
          Classifications: {'DNA': 29}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "L"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2591
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308}
          Chain breaks: 1
  Time building chain proxies: 3.76, per 1000 atoms: 0.26
  Number of scatterers: 14661
  At special positions: 0
  Unit cell: (98.707, 152.397, 130.921, 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      19     16.00
     P     293     15.00
     O    3314      8.00
     N    2722      7.00
     C    8313      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: 1.19
  Conformation dependent library (CDL) restraints added in 430.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      68.3% alpha, 4.5% beta
      142 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.848A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.567A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.758A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.531A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.602A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.547A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.538A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.798A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ARG E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.551A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.270A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.637A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.511A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.628A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 12 through 29
      removed outlier: 3.995A  pdb=" N   GLU L  21 " --> pdb=" O   ASP L  17 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU L  22 " --> pdb=" O   MET L  18 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN L  24 " --> pdb=" O   THR L  20 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE L  25 " --> pdb=" O   GLU L  21 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU L  26 " --> pdb=" O   LEU L  22 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 32 through 49
      removed outlier: 4.278A  pdb=" N   ALA L  38 " --> pdb=" O   HIS L  34 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  45 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 55 through 60
    Processing helix  chain 'L' and resid 66 through 80
    Processing helix  chain 'L' and resid 82 through 91
    Processing helix  chain 'L' and resid 91 through 102
    Processing helix  chain 'L' and resid 107 through 117
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 129 through 132
    Processing helix  chain 'L' and resid 133 through 142
    Processing helix  chain 'L' and resid 142 through 147
      removed outlier: 3.541A  pdb=" N   GLU L 147 " --> pdb=" O   PHE L 143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 152 through 170
    Processing helix  chain 'L' and resid 209 through 221
      removed outlier: 3.663A  pdb=" N   VAL L 214 " --> pdb=" O   LEU L 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 261 through 274
      removed outlier: 4.606A  pdb=" N   TYR L 266 " --> pdb=" O   LYS L 262 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   CYS L 267 " --> pdb=" O   ASP L 263 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY L 274 " --> pdb=" O   LEU L 270 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 275 through 289
    Processing helix  chain 'L' and resid 315 through 323
      removed outlier: 3.536A  pdb=" N   ILE L 323 " --> pdb=" O   ILE L 319 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 329 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.153A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.355A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.588A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.210A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.691A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151
      removed outlier: 3.604A  pdb=" N   ILE L 150 " --> pdb=" O   SER L 188 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER L 188 " --> pdb=" O   ILE L 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 177
      removed outlier: 3.733A  pdb=" N   ILE L 174 " --> pdb=" O   THR L 196 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL L 238 " --> pdb=" O   THR L 227 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   THR L 227 " --> pdb=" O   VAL L 238 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293

    527 hydrogen bonds defined for protein.
    1553 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      365 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3527
        1.34 -     1.46: 4367
        1.46 -     1.58: 7009
        1.58 -     1.70: 584
        1.70 -     1.82: 35
  Bond restraints: 15522
  Sorted by residual:
  bond pdb=" P    DC K 119 "
       pdb=" OP3  DC K 119 "
    ideal  model  delta    sigma   weight residual
    1.480  1.619 -0.139 2.00e-02 2.50e+03 4.83e+01
  bond pdb=" N   LYS G  36 "
       pdb=" CA  LYS G  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.94e+00
  bond pdb=" N   ASN F  25 "
       pdb=" CA  ASN F  25 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.42e-02 4.96e+03 6.11e+00
  bond pdb=" N   ARG L 254 "
       pdb=" CA  ARG L 254 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.29e-02 6.01e+03 5.53e+00
  bond pdb=" N   LYS L  84 "
       pdb=" CA  LYS L  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.79e+00
  ... (remaining 15517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 22135
        3.39 -     6.78: 52
        6.78 -    10.17: 8
       10.17 -    13.56: 1
       13.56 -    16.95: 2
  Bond angle restraints: 22198
  Sorted by residual:
  angle pdb=" C   LYS L  87 "
        pdb=" CA  LYS L  87 "
        pdb=" CB  LYS L  87 "
      ideal   model   delta    sigma   weight residual
     110.88   93.93   16.95 1.57e+00 4.06e-01 1.17e+02
  angle pdb=" CB  LYS L  87 "
        pdb=" CG  LYS L  87 "
        pdb=" CD  LYS L  87 "
      ideal   model   delta    sigma   weight residual
     111.30   94.87   16.43 2.30e+00 1.89e-01 5.10e+01
  angle pdb=" C   ASP G  72 "
        pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     122.83  115.63    7.20 1.54e+00 4.22e-01 2.19e+01
  angle pdb=" N   VAL E  46 "
        pdb=" CA  VAL E  46 "
        pdb=" C   VAL E  46 "
      ideal   model   delta    sigma   weight residual
     112.98  107.48    5.50 1.25e+00 6.40e-01 1.94e+01
  angle pdb=" N   ARG L 253 "
        pdb=" CA  ARG L 253 "
        pdb=" C   ARG L 253 "
      ideal   model   delta    sigma   weight residual
     109.24  102.53    6.71 1.67e+00 3.59e-01 1.62e+01
  ... (remaining 22193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.34: 6844
       28.34 -    56.68: 1607
       56.68 -    85.02: 167
       85.02 -   113.36: 5
      113.36 -   141.70: 4
  Dihedral angle restraints: 8627
    sinusoidal: 5476
      harmonic: 3151
  Sorted by residual:
  dihedral pdb=" C   LYS L  87 "
           pdb=" N   LYS L  87 "
           pdb=" CA  LYS L  87 "
           pdb=" CB  LYS L  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.49  -21.11     0      2.50e+00 1.60e-01 7.13e+01
  dihedral pdb=" N   LYS L  87 "
           pdb=" C   LYS L  87 "
           pdb=" CA  LYS L  87 "
           pdb=" CB  LYS L  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.47   11.33     0      2.50e+00 1.60e-01 2.05e+01
  dihedral pdb=" CA  GLU E  50 "
           pdb=" C   GLU E  50 "
           pdb=" N   ILE E  51 "
           pdb=" CA  ILE E  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.85   22.15     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 8624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 2494
       0.124 -    0.249: 8
       0.249 -    0.373: 1
       0.373 -    0.498: 2
       0.498 -    0.622: 2
  Chirality restraints: 2507
  Sorted by residual:
  chirality pdb=" P    DG J  30 "
            pdb=" OP1  DG J  30 "
            pdb=" OP2  DG J  30 "
            pdb=" O5'  DG J  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" P    DC K 119 "
            pdb=" OP1  DC K 119 "
            pdb=" OP2  DC K 119 "
            pdb=" O5'  DC K 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.97   -0.62 2.00e-01 2.50e+01 9.65e+00
  chirality pdb=" CA  LYS L  87 "
            pdb=" N   LYS L  87 "
            pdb=" C   LYS L  87 "
            pdb=" CB  LYS L  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.97   -0.46 2.00e-01 2.50e+01 5.31e+00
  ... (remaining 2504 not shown)

  Planarity restraints: 1802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  71 "   -0.647 9.50e-02 1.11e+02   2.90e-01 5.14e+01
        pdb=" NE  ARG G  71 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  71 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  71 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  71 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  68 "   -0.021 2.00e-02 2.50e+03   4.28e-02 1.83e+01
        pdb=" C   ASN G  68 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ASN G  68 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA G  69 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "    0.018 2.00e-02 2.50e+03   1.69e-02 5.70e+00
        pdb=" CG  TYR D  83 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1799 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3218
        2.81 -     3.33: 13195
        3.33 -     3.85: 28520
        3.85 -     4.38: 31766
        4.38 -     4.90: 46425
  Nonbonded interactions: 123124
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OE2 GLU C  41 "
            pdb=" OG  SER D  87 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   ASP L  17 "
            pdb=" OG1 THR L  20 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   LEU C  23 "
     model   vdw
     2.317 3.040
  ... (remaining 123119 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 32 or resid 34 through 81 or resid 83 through 124))
  selection = (chain 'H' and (resid 32 or resid 34 through 81 or resid 83 through 124))
}

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=0.50 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:             16.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.910
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     15.780
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
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      :  0.004   0.139  15522  Z= 0.177
  Angle     :  0.634  16.954  22198  Z= 0.366
  Chirality :  0.043   0.622   2507
  Planarity :  0.008   0.290   1802
  Dihedral  : 25.838 141.698   6597
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.98 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1067
  helix:  1.89 (0.20), residues: 702
  sheet:  1.41 (0.88), residues: 29
  loop : -0.28 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  79 
 TYR   0.042   0.002   TYR D  83 
 PHE   0.009   0.001   PHE D  65 
 TRP   0.003   0.001   TRP L 325 
 HIS   0.010   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (15522)
  covalent geometry    : angle       0.63436 (22198)
  hydrogen bonds       : bond        0.11620 (  892)
  hydrogen bonds       : angle       4.01131 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: A  120 MET cc_start: 0.7920 (mtm) cc_final: 0.7309 (mtp)
REVERT: C   36 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8590 (ttmt)
REVERT: C   61 GLU cc_start: 0.8133 (tp30) cc_final: 0.7861 (tp30)
REVERT: G  110 ASN cc_start: 0.8874 (t0) cc_final: 0.8649 (t0)
REVERT: L   72 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8330 (mptt)
REVERT: L  135 HIS cc_start: 0.8523 (t70) cc_final: 0.8303 (t-170)
REVERT: L  282 MET cc_start: -0.1462 (mmp) cc_final: -0.1741 (mmp)
REVERT: L  325 TRP cc_start: 0.7697 (t-100) cc_final: 0.7371 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1626
  time to fit residues: 35.0528
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   72 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.0370
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0970
   overall best weight:    1.4262

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

Flipped N/Q/H residues before XYZ refinement:
E  39 HIS
F  25 ASN
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.094773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.056522 restraints weight = 63332.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 2.69
r_work: 0.2787 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15522  Z= 0.155
  Angle     :  0.538   7.526  22198  Z= 0.314
  Chirality :  0.034   0.137   2507
  Planarity :  0.004   0.050   1802
  Dihedral  : 28.808 143.919   4410
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.39 %
    Favored  : 91.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.26), residues: 1067
  helix:  2.31 (0.20), residues: 726
  sheet:  1.30 (0.80), residues: 29
  loop : -0.29 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.033   0.002   TYR H  83 
 PHE   0.006   0.001   PHE D  65 
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (15522)
  covalent geometry    : angle       0.53781 (22198)
  hydrogen bonds       : bond        0.03537 (  892)
  hydrogen bonds       : angle       3.08220 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8662 (mt-10)
REVERT: A  120 MET cc_start: 0.8605 (mtm) cc_final: 0.8291 (mtp)
REVERT: C   36 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8857 (ttmt)
REVERT: C   61 GLU cc_start: 0.8875 (tp30) cc_final: 0.8554 (tp30)
REVERT: E   59 GLU cc_start: 0.8218 (pm20) cc_final: 0.7979 (pm20)
REVERT: G  110 ASN cc_start: 0.8956 (t0) cc_final: 0.8605 (t0)
REVERT: L  282 MET cc_start: -0.1101 (mmp) cc_final: -0.1341 (mmp)
REVERT: L  325 TRP cc_start: 0.7804 (t-100) cc_final: 0.7501 (t-100)
  outliers start: 7
  outliers final: 6
  residues processed: 131
  average time/residue: 0.1497
  time to fit residues: 27.2716
Evaluate side-chains
  124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue  255 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 54 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9980
   chunk 122 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 111 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 116 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   overall best weight:    5.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
E  39 HIS
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.090667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.051714 restraints weight = 83659.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.02
r_work: 0.2638 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053  15522  Z= 0.343
  Angle     :  0.639   6.896  22198  Z= 0.367
  Chirality :  0.040   0.145   2507
  Planarity :  0.004   0.044   1802
  Dihedral  : 29.316 146.977   4406
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.76 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.02 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.26), residues: 1067
  helix:  2.11 (0.19), residues: 726
  sheet:  1.74 (0.85), residues: 29
  loop : -0.52 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  83 
 TYR   0.066   0.003   TYR H  83 
 PHE   0.010   0.001   PHE C  25 
 TRP   0.003   0.001   TRP L 325 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00789 (15522)
  covalent geometry    : angle       0.63914 (22198)
  hydrogen bonds       : bond        0.04749 (  892)
  hydrogen bonds       : angle       3.33364 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.470 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8913 (ttmt)
REVERT: C   61 GLU cc_start: 0.8995 (tp30) cc_final: 0.8785 (tp30)
REVERT: C  110 ASN cc_start: 0.9183 (t0) cc_final: 0.8936 (t0)
REVERT: E   59 GLU cc_start: 0.8444 (pm20) cc_final: 0.8106 (pm20)
REVERT: E  107 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9150 (t)
REVERT: L  325 TRP cc_start: 0.7748 (t-100) cc_final: 0.7414 (t-100)
  outliers start: 12
  outliers final: 8
  residues processed: 124
  average time/residue: 0.1336
  time to fit residues: 23.3396
Evaluate side-chains
  123 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 104 optimal weight:   40.0000
   chunk 116 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.093207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.054977 restraints weight = 70259.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 2.78
r_work: 0.2741 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15522  Z= 0.157
  Angle     :  0.535   6.857  22198  Z= 0.316
  Chirality :  0.034   0.141   2507
  Planarity :  0.004   0.048   1802
  Dihedral  : 29.073 148.965   4406
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.00 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.43 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.26), residues: 1067
  helix:  2.38 (0.19), residues: 726
  sheet:  1.48 (0.79), residues: 29
  loop : -0.43 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  79 
 TYR   0.046   0.002   TYR D  83 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.004   0.001   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (15522)
  covalent geometry    : angle       0.53521 (22198)
  hydrogen bonds       : bond        0.03425 (  892)
  hydrogen bonds       : angle       2.94665 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.356 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8879 (ttmt)
REVERT: C   61 GLU cc_start: 0.8896 (tp30) cc_final: 0.8633 (tp30)
REVERT: C  110 ASN cc_start: 0.9105 (t0) cc_final: 0.8887 (t0)
REVERT: E   59 GLU cc_start: 0.8214 (pm20) cc_final: 0.7744 (pm20)
REVERT: L  236 MET cc_start: 0.9064 (mpp) cc_final: 0.8823 (mmp)
REVERT: L  325 TRP cc_start: 0.7864 (t-100) cc_final: 0.7550 (t-100)
  outliers start: 10
  outliers final: 6
  residues processed: 125
  average time/residue: 0.1514
  time to fit residues: 25.9584
Evaluate side-chains
  123 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 103 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 128 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.092466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.053125 restraints weight = 72092.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 2.96
r_work: 0.2730 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  15522  Z= 0.204
  Angle     :  0.552   7.247  22198  Z= 0.325
  Chirality :  0.035   0.140   2507
  Planarity :  0.004   0.045   1802
  Dihedral  : 29.162 149.450   4406
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.09 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.26), residues: 1067
  helix:  2.33 (0.19), residues: 727
  sheet:  1.44 (0.78), residues: 29
  loop : -0.48 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG G  35 
 TYR   0.057   0.002   TYR D  83 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.002   0.001   TRP L 325 
 HIS   0.006   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (15522)
  covalent geometry    : angle       0.55247 (22198)
  hydrogen bonds       : bond        0.03830 (  892)
  hydrogen bonds       : angle       3.01309 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8901 (ttmt)
REVERT: C   41 GLU cc_start: 0.8440 (pp20) cc_final: 0.8230 (tm-30)
REVERT: C   61 GLU cc_start: 0.8907 (tp30) cc_final: 0.8657 (tp30)
REVERT: C  110 ASN cc_start: 0.9134 (t0) cc_final: 0.8895 (t0)
REVERT: E   59 GLU cc_start: 0.8353 (pm20) cc_final: 0.7831 (pm20)
REVERT: L   69 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9354 (tt)
REVERT: L  236 MET cc_start: 0.9126 (mpp) cc_final: 0.8876 (mmp)
REVERT: L  325 TRP cc_start: 0.7870 (t-100) cc_final: 0.7487 (t-100)
  outliers start: 12
  outliers final: 8
  residues processed: 125
  average time/residue: 0.1658
  time to fit residues: 28.5483
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 125 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 123 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.093439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.054920 restraints weight = 68402.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.84
r_work: 0.2785 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15522  Z= 0.141
  Angle     :  0.527   7.711  22198  Z= 0.312
  Chirality :  0.033   0.139   2507
  Planarity :  0.004   0.050   1802
  Dihedral  : 29.075 150.335   4406
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.29 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.07 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.26), residues: 1067
  helix:  2.45 (0.19), residues: 720
  sheet:  1.32 (0.76), residues: 29
  loop : -0.35 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  35 
 TYR   0.039   0.002   TYR H  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.003   0.001   TRP L 325 
 HIS   0.006   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15522)
  covalent geometry    : angle       0.52671 (22198)
  hydrogen bonds       : bond        0.03346 (  892)
  hydrogen bonds       : angle       2.87455 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8872 (ttmt)
REVERT: C   41 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8148 (tm-30)
REVERT: C   61 GLU cc_start: 0.8844 (tp30) cc_final: 0.8568 (tp30)
REVERT: E   58 THR cc_start: 0.9064 (p) cc_final: 0.8690 (p)
REVERT: E   59 GLU cc_start: 0.8226 (pm20) cc_final: 0.7668 (pm20)
REVERT: L   69 ILE cc_start: 0.9731 (OUTLIER) cc_final: 0.9354 (tt)
REVERT: L  236 MET cc_start: 0.9119 (mpp) cc_final: 0.8856 (mmp)
REVERT: L  325 TRP cc_start: 0.7901 (t-100) cc_final: 0.7461 (t-100)
  outliers start: 10
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1426
  time to fit residues: 25.3942
Evaluate side-chains
  125 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 122 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 116 optimal weight:   30.0000
   chunk 27 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.093876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.055190 restraints weight = 88426.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 3.33
r_work: 0.2766 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15522  Z= 0.142
  Angle     :  0.527   7.851  22198  Z= 0.312
  Chirality :  0.033   0.140   2507
  Planarity :  0.004   0.049   1802
  Dihedral  : 29.055 150.481   4406
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.17 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.26), residues: 1067
  helix:  2.46 (0.20), residues: 720
  sheet:  1.35 (0.76), residues: 29
  loop : -0.32 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG G  35 
 TYR   0.045   0.002   TYR D  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.002   0.001   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15522)
  covalent geometry    : angle       0.52720 (22198)
  hydrogen bonds       : bond        0.03356 (  892)
  hydrogen bonds       : angle       2.85796 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8892 (ttmt)
REVERT: C   41 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8173 (tm-30)
REVERT: C   61 GLU cc_start: 0.8871 (tp30) cc_final: 0.8608 (tp30)
REVERT: E   58 THR cc_start: 0.9054 (p) cc_final: 0.8687 (p)
REVERT: E   59 GLU cc_start: 0.8312 (pm20) cc_final: 0.7766 (pm20)
REVERT: L   69 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9352 (tt)
REVERT: L  236 MET cc_start: 0.9131 (mpp) cc_final: 0.8897 (mmp)
REVERT: L  325 TRP cc_start: 0.7879 (t-100) cc_final: 0.7497 (t-100)
  outliers start: 14
  outliers final: 9
  residues processed: 129
  average time/residue: 0.1541
  time to fit residues: 27.6516
Evaluate side-chains
  129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 127 optimal weight:   30.0000
   chunk 128 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.093531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.054530 restraints weight = 79341.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.09
r_work: 0.2763 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15522  Z= 0.167
  Angle     :  0.542   7.417  22198  Z= 0.320
  Chirality :  0.034   0.140   2507
  Planarity :  0.004   0.047   1802
  Dihedral  : 29.077 150.573   4406
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.04 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 1067
  helix:  2.43 (0.20), residues: 720
  sheet:  1.29 (0.77), residues: 29
  loop : -0.36 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  35 
 TYR   0.054   0.002   TYR H  83 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (15522)
  covalent geometry    : angle       0.54203 (22198)
  hydrogen bonds       : bond        0.03532 (  892)
  hydrogen bonds       : angle       2.88181 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7865 (mt)
REVERT: C   36 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8897 (ttmt)
REVERT: C   41 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8223 (tm-30)
REVERT: C   61 GLU cc_start: 0.8877 (tp30) cc_final: 0.8613 (tp30)
REVERT: C  110 ASN cc_start: 0.9119 (t0) cc_final: 0.8895 (t0)
REVERT: E   58 THR cc_start: 0.9068 (p) cc_final: 0.8694 (p)
REVERT: E   59 GLU cc_start: 0.8323 (pm20) cc_final: 0.7762 (pm20)
REVERT: G   36 LYS cc_start: 0.9135 (tppt) cc_final: 0.8628 (tttt)
REVERT: L   69 ILE cc_start: 0.9734 (OUTLIER) cc_final: 0.9365 (tt)
REVERT: L  236 MET cc_start: 0.9141 (mpp) cc_final: 0.8914 (mmp)
REVERT: L  325 TRP cc_start: 0.7873 (t-100) cc_final: 0.7510 (t-100)
  outliers start: 10
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1605
  time to fit residues: 28.3325
Evaluate side-chains
  129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0020
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 28 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8990

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.094546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.055924 restraints weight = 75622.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 3.03
r_work: 0.2799 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15522  Z= 0.142
  Angle     :  0.532   7.154  22198  Z= 0.315
  Chirality :  0.033   0.140   2507
  Planarity :  0.004   0.050   1802
  Dihedral  : 29.024 150.968   4406
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.26 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.27), residues: 1067
  helix:  2.46 (0.20), residues: 720
  sheet:  1.21 (0.77), residues: 29
  loop : -0.32 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  35 
 TYR   0.065   0.002   TYR H  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.002   0.000   TRP L 325 
 HIS   0.007   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15522)
  covalent geometry    : angle       0.53171 (22198)
  hydrogen bonds       : bond        0.03390 (  892)
  hydrogen bonds       : angle       2.83428 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8872 (ttmt)
REVERT: C   41 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8161 (tm-30)
REVERT: C   61 GLU cc_start: 0.8852 (tp30) cc_final: 0.8562 (tp30)
REVERT: E   58 THR cc_start: 0.9025 (p) cc_final: 0.8650 (p)
REVERT: E   59 GLU cc_start: 0.8276 (pm20) cc_final: 0.7710 (pm20)
REVERT: G   36 LYS cc_start: 0.9135 (tppt) cc_final: 0.8607 (tttt)
REVERT: L   69 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9363 (tt)
REVERT: L  236 MET cc_start: 0.9144 (mpp) cc_final: 0.8919 (mmp)
REVERT: L  325 TRP cc_start: 0.7898 (t-100) cc_final: 0.7529 (t-100)
  outliers start: 11
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1607
  time to fit residues: 28.7561
Evaluate side-chains
  126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Chi-restraints excluded: chain L residue  129 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 115 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.092695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.054137 restraints weight = 79896.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 3.05
r_work: 0.2752 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15522  Z= 0.201
  Angle     :  0.561   7.349  22198  Z= 0.329
  Chirality :  0.035   0.141   2507
  Planarity :  0.004   0.045   1802
  Dihedral  : 29.147 151.136   4406
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.57 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.70 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 1067
  helix:  2.42 (0.20), residues: 721
  sheet:  1.35 (0.77), residues: 29
  loop : -0.36 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  35 
 TYR   0.052   0.002   TYR D  83 
 PHE   0.006   0.001   PHE D  65 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.016   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (15522)
  covalent geometry    : angle       0.56076 (22198)
  hydrogen bonds       : bond        0.03831 (  892)
  hydrogen bonds       : angle       2.95697 ( 2283)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8884 (ttmt)
REVERT: C   41 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8158 (tm-30)
REVERT: C   61 GLU cc_start: 0.8883 (tp30) cc_final: 0.8640 (tp30)
REVERT: C  110 ASN cc_start: 0.9125 (t0) cc_final: 0.8888 (t0)
REVERT: E   58 THR cc_start: 0.9078 (p) cc_final: 0.8715 (p)
REVERT: E   59 GLU cc_start: 0.8421 (pm20) cc_final: 0.7882 (pm20)
REVERT: G   36 LYS cc_start: 0.9158 (tppt) cc_final: 0.8662 (tttt)
REVERT: L   69 ILE cc_start: 0.9733 (OUTLIER) cc_final: 0.9392 (tt)
REVERT: L  236 MET cc_start: 0.9151 (mpp) cc_final: 0.8907 (mmp)
REVERT: L  325 TRP cc_start: 0.7870 (t-100) cc_final: 0.7483 (t-100)
  outliers start: 13
  outliers final: 9
  residues processed: 130
  average time/residue: 0.1647
  time to fit residues: 29.8157
Evaluate side-chains
  132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue   69 ILE
Chi-restraints excluded: chain L residue  129 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 100 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 130 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.093897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.055396 restraints weight = 79695.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.06
r_work: 0.2790 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15522  Z= 0.147
  Angle     :  0.544   8.125  22198  Z= 0.320
  Chirality :  0.033   0.140   2507
  Planarity :  0.003   0.049   1802
  Dihedral  : 29.058 151.365   4406
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.91 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.27), residues: 1067
  helix:  2.47 (0.20), residues: 720
  sheet:  1.37 (0.78), residues: 29
  loop : -0.31 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG G  35 
 TYR   0.049   0.002   TYR F  88 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.002   0.000   TRP L 325 
 HIS   0.006   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (15522)
  covalent geometry    : angle       0.54407 (22198)
  hydrogen bonds       : bond        0.03493 (  892)
  hydrogen bonds       : angle       2.86754 ( 2283)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7491.03 seconds
wall clock time: 127 minutes 45.34 seconds (7665.34 seconds total)